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Miller KJ, Box WG, Boulton CA, Smart KA. Cell Cycle Synchrony of Propagated and Recycled Lager Yeast and its Impact on Lag Phase in Fermenter. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2011-1216-01] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Katherine J. Miller
- Division of Food Sciences, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Wendy G. Box
- Division of Food Sciences, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Christopher A. Boulton
- Division of Food Sciences, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Katherine A. Smart
- Division of Food Sciences, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough, LE12 5RD, UK
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2
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Fernandes LD, Guseva K, de Moura APS. Cooperative response and clustering: Consequences of membrane-mediated interactions among mechanosensitive channels. Phys Rev E 2017; 96:022410. [PMID: 28950473 DOI: 10.1103/physreve.96.022410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Indexed: 11/07/2022]
Abstract
Mechanosensitive channels are ion channels which act as cells' safety valves, opening when the osmotic pressure becomes too high and making cells avoid damage by releasing ions. They are found on the cellular membrane of a large number of organisms. They interact with each other by means of deformations they induce in the membrane. We show that collective dynamics arising from the interchannel interactions lead to first- and second-order phase transitions in the fraction of open channels in equilibrium relating to the formation of channel clusters. We show that this results in a considerable delay of the response of cells to osmotic shocks, and to an extreme cell-to-cell stochastic variations in their response times, despite the large numbers of channels present in each cell. We discuss how our results are relevant for E. coli.
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Affiliation(s)
- Lucas D Fernandes
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura Luiz de Queiroz - Universidade de São Paulo (USP), 13418-900, Piracicaba, São Paulo, Brazil
| | - Ksenia Guseva
- Theoretical Physics/Complex Systems, ICBM, University of Oldenburg, 26129 Oldenburg, Germany
| | - Alessandro P S de Moura
- Institute for Complex Systems and Mathematical Biology, King's College, University of Aberdeen, AB24 3UE, Aberdeen, United Kingdom
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3
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Carmona L, Varela J, Godoy L, Ganga MA. Comparative proteome analysis of Brettanomyces bruxellensis under hydroxycinnamic acid growth. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Li X, Wang L, Li Y, Fu J, Zhen L, Yang Q, Li S, Zhang Y. Tyrosine phosphorylation of dihydrolipoamide dehydrogenase as a potential cadmium target and its inhibitory role in regulating mouse sperm motility. Toxicology 2016; 357-358:52-64. [PMID: 27289041 DOI: 10.1016/j.tox.2016.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/06/2016] [Accepted: 06/06/2016] [Indexed: 01/19/2023]
Abstract
Cadmium (Cd) is reported to reduce sperm motility and functions. However, the molecular mechanisms of Cd-induced toxicity remain largely unknown, presenting a major knowledge gap in research on reproductive toxicology. In the present study, we identified a candidate protein, dihydrolipoamide dehydrogenase (DLD), which is a post-pyruvate metabolic enzyme, exhibiting tyrosine phosphorylation in mouse sperm exposed to Cd both in vivo and in vitro. Immunoprecipitation assay demonstrated DLD was phosphorylated in tyrosine residues without altered expression after Cd treatment, which further confirmed our identified result. However, the tyrosine phosphorylation of DLD did not participate in mouse sperm capacitation and Bovine Serum Albumin (BSA) effectively prevented the tyrosine phosphorylation of DLD. Moreover, Cd-induced tyrosine phosphorylation of DLD lowered its dehydrogenase activity and meanwhile, Nicotinamide Adenine Dinucleotide Hydrogen (NADH) content, Adenosine Triphosphate (ATP) production and sperm motility were all inhibited by Cd. Interestingly, when the tyrosine phosphorylation of DLD was blocked by BSA, the decrease of DLD activity, NADH and ATP content as well as sperm motility was also suppressed simultaneously. These results suggested that Cd-induced tyrosine phosphorylation of DLD inhibited its activity and thus suppressed the tricarboxylic acid (TCA) cycle, which resulted in the reduction of NADH and hence the ATP production generated through oxidative phosphorylation (OPHOXS). Taken together, our results revealed that Cd induced DLD tyrosine phosphorylation, in response to regulate TCA metabolic pathway, which reduced ATP levels and these negative effects led to decreased sperm motility. This study provided new understanding of the mechanisms contributing to the harmful effects of Cd on the motility and function of spermatozoa.
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Affiliation(s)
- Xinhong Li
- Shanghai Key Lab of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 200240, China.
| | - Lirui Wang
- Shanghai Key Lab of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 200240, China
| | - Yuhua Li
- Shanghai Key Lab of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 200240, China
| | - Jieli Fu
- Shanghai Key Lab of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 200240, China
| | - Linqing Zhen
- Shanghai Key Lab of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 200240, China
| | - Qiangzhen Yang
- Shanghai Key Lab of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 200240, China
| | - Sisi Li
- Shanghai Key Lab of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 200240, China
| | - Yukun Zhang
- Shanghai Key Lab of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 200240, China
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Chen JA, Chang LR, Feng GM, Lee ST, Hsieh CY, Jeng SF, Huang WS. Stress alters the expression of aquaporins in cultured rat intestinal epithelial cells. Exp Ther Med 2015; 10:1967-1972. [PMID: 26640581 DOI: 10.3892/etm.2015.2771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 09/01/2015] [Indexed: 12/24/2022] Open
Abstract
Aquaporins (AQPs) are widely-expressed small water channel proteins that provide the major route for water transport across plasma membranes in various cell types. Although the quantity of water transported in the intestinal tract is second only to that in the kidney, the precise role of AQPs in this organ remains largely uncertain. The present study reports the effects of hypertonic stress and ischemia/reperfusion injury on the expression of AQPs in intestinal epithelial cells. Cultured rat intestinal epithelial cells were incubated in 300 mM mannitol-containing, hypertonic culture medium or subjected to simulated ischemia/reperfusion treatment. The cell viability was evaluated by MTT assay, and the expression of AQPs was determined by semi-quantitative reverse transcription polymerase chain reaction and western blotting. Despite reduced viability, the cells exposed to hypertonic stress for 16 h demonstrated enhanced expression of AQP1 mRNA and protein. AQP9 and glycosylated AQP11 proteins were also markedly upregulated. Ischemia alone did not affect the cell viability, but subsequent reperfusion significantly reduced viability. The mRNA expression levels of all the tested AQPs were not altered by ischemia alone or by ischemia/reperfusion; however, AQP8 protein was markedly reduced by ischemic injury. In addition, treatment with ischemia alone eradicated the normally-expressed, non-glycosylated AQP11 protein whilst inducing pronounced expression of the glycosylated form. These observations may indicate that AQPs function in the intestinal epithelia in response to stress.
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Affiliation(s)
- Jian-An Chen
- Division of Plastic Surgery, Kaohsiung Armed Forces General Hospital, Kaohsiung 802, Taiwan, R.O.C. ; Department of Plastic Surgery, E-DA Hospital, Kaohsiung 824, Taiwan, R.O.C
| | - Li-Ren Chang
- Department of Plastic Surgery, E-DA Hospital, Kaohsiung 824, Taiwan, R.O.C
| | - Guan-Ming Feng
- Department of Plastic Surgery, E-DA Hospital, Kaohsiung 824, Taiwan, R.O.C
| | - Shu-Ting Lee
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung 802, Taiwan, R.O.C
| | - Chien-Yan Hsieh
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung 802, Taiwan, R.O.C
| | - Seng-Feng Jeng
- Department of Plastic Surgery, E-DA Hospital, Kaohsiung 824, Taiwan, R.O.C
| | - Wen-Shyan Huang
- Division of Plastic Surgery, Kaohsiung Armed Forces General Hospital Zuoying Branch, Kaohsiung 813, Taiwan, R.O.C. ; Department of Surgery, National Defense Medical Center, Taipei 114, Taiwan, R.O.C
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García-Ríos E, López-Malo M, Guillamón JM. Global phenotypic and genomic comparison of two Saccharomyces cerevisiae wine strains reveals a novel role of the sulfur assimilation pathway in adaptation at low temperature fermentations. BMC Genomics 2014; 15:1059. [PMID: 25471357 PMCID: PMC4265444 DOI: 10.1186/1471-2164-15-1059] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/26/2014] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The wine industry needs better-adapted yeasts to grow at low temperature because it is interested in fermenting at low temperature to improve wine aroma. Elucidating the response to cold in Saccharomyces cerevisiae is of paramount importance for the selection or genetic improvement of wine strains. RESULTS We followed a global approach by comparing transcriptomic, proteomic and genomic changes in two commercial wine strains, which showed clear differences in their growth and fermentation capacity at low temperature. These strains were selected according to the maximum growth rate in a synthetic grape must during miniaturized batch cultures at different temperatures. The fitness differences of the selected strains were corroborated by directly competing during fermentations at optimum and low temperatures. The up-regulation of the genes of the sulfur assimilation pathway and glutathione biosynthesis suggested a crucial role in better performance at low temperature. The presence of some metabolites of these pathways, such as S-Adenosilmethionine (SAM) and glutathione, counteracted the differences in growth rate at low temperature in both strains. Generally, the proteomic and genomic changes observed in both strains also supported the importance of these metabolic pathways in adaptation at low temperature. CONCLUSIONS This work reveals a novel role of the sulfur assimilation pathway in adaptation at low temperature. We propose that a greater activation of this metabolic route enhances the synthesis of key metabolites, such as glutathione, whose protective effects can contribute to improve the fermentation process.
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Affiliation(s)
- Estéfani García-Ríos
- />Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, Po Box 73E-46100, Paterna Valencia, Spain
| | - María López-Malo
- />Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, Po Box 73E-46100, Paterna Valencia, Spain
- />Biotecnologia Enològica. Departament de Bioquímica i Biotecnologia, Facultat de Enologia, Universitat Rovira i Virgili, Marcel•li Domingo s/n, 43007 Tarragona, Spain
| | - José Manuel Guillamón
- />Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, Po Box 73E-46100, Paterna Valencia, Spain
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7
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Salvadó Z, Chiva R, Rozès N, Cordero-Otero R, Guillamón JM. Functional analysis to identify genes in wine yeast adaptation to low-temperature fermentation. J Appl Microbiol 2012; 113:76-88. [PMID: 22507142 DOI: 10.1111/j.1365-2672.2012.05308.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AIMS To identify genes and proteins involved in adaptation to low-temperature fermentations in a commercial wine yeast. METHODS AND RESULTS Nine proteins were identified as representing the most significant changes in proteomic maps during the first 24 h of fermentation at low (13°C) and standard temperature (25°C). These proteins were mainly involved in stress response and in glucose and nitrogen metabolism. Transcription analysis of the genes encoding most of these proteins within the same time frame of wine fermentation presented a good correlation with proteomic data. Knockout and overexpressing strains of some of these genes were constructed and tested to evaluate their ability to start the fermentation process. The strain overexpressing ILV5 improved its fermentation activity in the first hours of fermentation. This strain showed a quicker process of mitochondrial degeneration, an altered intracellular amino acid profile and laxer nitrogen catabolite repression regulation. CONCLUSIONS The proteomic and transcriptomic analysis is useful to detect key molecular adaptation mechanisms of biotechnological interest for industrial processes. ILV5 gene seems to be important in wine yeast adaptation to low-temperature fermentation. SIGNIFICANCE AND IMPACT OF THE STUDY This study provides information that might help improve the future performance of wine yeast, either by genetic modification or by adaptation during industrial production.
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Affiliation(s)
- Z Salvadó
- Biotecnologia Enològica, Departament de Bioquímica i Biotecnologia, Facultat de Enologia, Universitat Rovira i Virgili, Tarragona, Spain
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8
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Molecular basis of transport and regulation in the Na+/betaine symporter BetP. Nature 2009; 458:47-52. [DOI: 10.1038/nature07819] [Citation(s) in RCA: 274] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Accepted: 01/21/2009] [Indexed: 11/08/2022]
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Abstract
Under normal physiological conditions, the brain utilizes only a small number of carbon sources for energy. Recently, there is growing molecular and biochemical evidence that other carbon sources, including fructose, may play a role in neuro-energetics. Fructose is the number one commercial sweetener in Western civilization with large amounts of fructose being toxic, yet fructose metabolism remains relatively poorly characterized. Fructose is purportedly metabolized via either of two pathways, the fructose-1-phosphate pathway and/or the fructose-6-phosphate pathway. Many early metabolic studies could not clearly discriminate which of these two pathways predominates, nor could they distinguish which cell types in various tissues are capable of fructose metabolism. In addition, the lack of good physiological models, the diet-induced changes in gene expression in many tissues, the involvement of multiple genes in multiple pathways involved in fructose metabolism, and the lack of characterization of some genes involved in fructose metabolism have complicated our understanding of the physiological role of fructose in neuro-energetics. A recent neuro-metabolism study of the cerebellum demonstrated fructose metabolism and co-expression of the genes specific for the fructose 1-phosphate pathway, GLUT5 (glut5) and ketohexokinase (khk), in Purkinje cells suggesting this as an active pathway in specific neurons? Meanwhile, concern over the rapid increase in dietary fructose, particularly among children, has increased awareness about how fructose is metabolized in vivo and what effects a high fructose diet might have. In this regard, establishment of cellular and molecular studies and physiological characterization of the important and/or deleterious roles fructose plays in the brain is critical. This review will discuss the status of fructose metabolism in the brain with special reference to the cerebellum and the physiological roles of the different pathways.
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Affiliation(s)
- Vincent A Funari
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
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Cordier H, Mendes F, Vasconcelos I, François JM. A metabolic and genomic study of engineered Saccharomyces cerevisiae strains for high glycerol production. Metab Eng 2007; 9:364-78. [PMID: 17500021 DOI: 10.1016/j.ymben.2007.03.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2006] [Revised: 01/15/2007] [Accepted: 03/29/2007] [Indexed: 10/23/2022]
Abstract
Towards a global objective to produce chemical derivatives by microbial processes, this work dealt with a metabolic engineering of the yeast Saccharomyces cerevisiae for glycerol production. To accomplish this goal, overexpression of GPD1 was introduced in a tpi1delta mutant defective in triose phosphate isomerase. This strategy alleviated the inositol-less phenotype of this mutant, by reducing the levels of dihydroxyacetone phosphate and glycerol-3-P, two potent inhibitors of myo-inositol synthase that catalyzes the formation of inositol-6-phosphate from glucose-6-phosphate. Further deletion of ADH1 and overexpression of ALD3, encoding, respectively, the major NAD+-dependent alcohol dehydrogenase and a cytosolic NAD+-dependent aldehyde dehydrogenase yielded a yeast strain able to produce 0.46 g glycerol (g glucose)(-1) at a maximal rate of 3.1 mmol (g dry mass)(-1) h(-1) in aerated batch cultures. At the metabolic level, this genetic strategy shifted the flux control coefficient of the pathway to the level of the glycerol efflux, with a consequent intracellular accumulation of glycerol that could be partially reduced by the overproduction of glycerol exporter encoded by FPS1. At the transcriptomic level, this metabolic reprogramming brought about the upregulation of genes encoding NAD+/NADP+ binding proteins, a partial derepression of genes coding for TCA cycle and respiratory enzymes, and a downregulation of genes implicated in protein biosynthesis and ribosome biogenesis. Altogether, these metabolic and molecular alterations stand for major hurdles that may represent potential targets for further optimizing glycerol production in yeast.
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Affiliation(s)
- Hélène Cordier
- Laboratoire de Biotechnologie et Bioprocédés, UMR-CNRS 5504 & INRA 792, Toulouse, France
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Wojda I, Bebelman JP, Jakubowicz T, Siderius M. Thermosensitivity of the Saccharomyces cerevisiae gpp1gpp2 double deletion strain can be reduced by overexpression of genes involved in cell wall maintenance. Arch Microbiol 2007; 188:175-84. [PMID: 17390123 DOI: 10.1007/s00203-007-0234-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 02/26/2007] [Accepted: 03/05/2007] [Indexed: 02/08/2023]
Abstract
A Saccharomyces cerevisiae strain in which the GPP1 and GPP2 genes, both encoding glycerol-3-phosphate phosphatase isoforms, are deleted, displays both osmo- and thermosensitive (ts) phenotypes. We isolated genes involved in cell wall maintenance as multicopy suppressors of the gpp1gpp2 ts phenotype. We found that the gpp1gpp2 strain is hypersensitive to cell wall stress such as treatment with beta-1,3-glucanase containing cocktail Zymolyase and chitin-binding dye Calcofluor-white (CFW). Sensitivity to Zymolyase was rescued by overexpression of SSD1, while CFW sensitivity was rescued by SSD1, FLO8 and WSC3-genes isolated as multicopy suppressors of the gpp1gpp2 ts phenotype. Some of the isolated suppressor genes (SSD1, FLO8) also rescued the lytic phenotype of slt2 deletion strain. Additionally, the sensitivity to CFW was reduced when the cells were supplied with glycerol. Both growth on glycerol-based medium and overexpression of SSD1, FLO8 or WSC3 had additive suppressing effect on CFW sensitivity of the gpp1gpp2 mutant strain. We also confirmed that the internal glycerol level changed in cells exposed to cell wall perturbation.
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Affiliation(s)
- Iwona Wojda
- Department of Invertebrate Immunology, Institute of Biology, Maria Curie-Sklodowska University, Akademicka 19, 20-033, Lublin, Poland.
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13
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Smart KA. Brewing yeast genomes and genome-wide expression and proteome profiling during fermentation. Yeast 2007; 24:993-1013. [PMID: 17879324 DOI: 10.1002/yea.1553] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The genome structure, ancestry and instability of the brewing yeast strains have received considerable attention. The hybrid nature of brewing lager yeast strains provides adaptive potential but yields genome instability which can adversely affect fermentation performance. The requirement to differentiate between production strains and assess master cultures for genomic instability has led to significant adoption of specialized molecular tool kits by the industry. Furthermore, the development of genome-wide transcriptional and protein expression technologies has generated significant interest from brewers. The opportunity presented to explore, and the concurrent requirement to understand both, the constraints and potential of their strains to generate existing and new products during fermentation is discussed.
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Affiliation(s)
- Katherine A Smart
- Division of Food Sciences, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK.
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Tang JB, Chen YH. Identification of a tyrosine-phosphorylated CCCTC-binding nuclear factor in capacitated mouse spermatozoa. Proteomics 2006; 6:4800-7. [PMID: 16878297 DOI: 10.1002/pmic.200600256] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The molecular basis of mammalian sperm capacitation, either in vivo in the female reproductive tract, or in vitro, is poorly understood. It is well known that sperm capacitation is associated with an increase in tyrosine phosphorylation of a subset of proteins. We resolved the phosphoproteins in the cell lysate of mouse sperm after capacitation by 2-DE. One tyrosine-phosphorylated 130-kDa spot was trypsin-digested, and six oligopeptide sequences were established from the MS data. These were confirmed in a CCCTC-binding nuclear factor (CTCF), a widely expressed and highly conserved protein. Further, both an anti-phosphotyrosine antibody and an anti-CTCF antibody showed immunoreactivity to a 130-kDa component in the immunoprecipitates obtained after incubation of the cell lysate from the capacitated sperm using another anti-CTCF antibody. The data support the presence of a tyrosine-phosphorylated CTCF in the capacitated sperm. Immunolocalization of the CTCF revealed fluorescent staining in the acrosome region in both capacitated and incapacitated sperm. The electrophoretic mobility shift assay, using a CTCF target sequence 5'-GGCGGCGCCGCTAGGGGTCTCTCT-3' found in the promoter of the amyloid beta-protein precursor, manifested that, relative to CTCF in the incapacitated sperm, the tyrosine-phosphorylated protein in the capacitated sperm had stronger affinity to the CTCF target sequence.
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Affiliation(s)
- Jyh-Bing Tang
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
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15
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Zuzuarregui A, Monteoliva L, Gil C, del Olmo ML. Transcriptomic and proteomic approach for understanding the molecular basis of adaptation of Saccharomyces cerevisiae to wine fermentation. Appl Environ Microbiol 2006; 72:836-47. [PMID: 16391125 PMCID: PMC1352203 DOI: 10.1128/aem.72.1.836-847.2006] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Accepted: 11/01/2005] [Indexed: 11/20/2022] Open
Abstract
Throughout alcoholic fermentation, Saccharomyces cerevisiae cells have to cope with several stress conditions that could affect their growth and viability. In addition, the metabolic activity of yeast cells during this process leads to the production of secondary compounds that contribute to the organoleptic properties of the resulting wine. Commercial strains have been selected during the last decades for inoculation into the must to carry out the alcoholic fermentation on the basis of physiological traits, but little is known about the molecular basis of the fermentative behavior of these strains. In this work, we present the first transcriptomic and proteomic comparison between two commercial strains with different fermentative behaviors. Our results indicate that some physiological differences between the fermentative behaviors of these two strains could be related to differences in the mRNA and protein profiles. In this sense, at the level of gene expression, we have found differences related to carbohydrate metabolism, nitrogen catabolite repression, and response to stimuli, among other factors. In addition, we have detected a relative increase in the abundance of proteins involved in stress responses (the heat shock protein Hsp26p, for instance) and in fermentation (in particular, the major cytosolic aldehyde dehydrogenase Ald6p) in the strain with better behavior during vinification. Moreover, in the case of the other strain, higher levels of enzymes required for sulfur metabolism (Cys4p, Hom6p, and Met22p) are observed, which could be related to the production of particular organoleptic compounds or to detoxification processes.
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Affiliation(s)
- Aurora Zuzuarregui
- Departament de Bioquímica i Biologia Molecular, Facultat de Ciències Biològiques, Universitat de València, Dr. Moliner, 50, E-46100 Burjassot (Valencia), Spain
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16
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Bleve G, Zacheo G, Cappello M, Dellaglio F, Grieco F. Subcellular localization and functional expression of the glycerol uptake protein 1 (GUP1) of Saccharomyces cerevisiae tagged with green fluorescent protein. Biochem J 2005; 390:145-55. [PMID: 15813700 PMCID: PMC1184570 DOI: 10.1042/bj20042045] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
GFP (green fluorescent protein) from Aequorea victoria was used as an in vivo reporter protein when fused to the N- and C-termini of the glycerol uptake protein 1 (Gup1p) of Saccharomyces cerevisiae. The subcellular localization and functional expression of biologically active Gup1-GFP chimaeras was monitored by confocal laser scanning and electron microscopy, thus supplying the first study of GUP1 dynamics in live yeast cells. The Gup1p tagged with GFP is a functional glycerol transporter localized at the plasma membrane and endoplasmic reticulum levels of induced cells. The factors involved in proper localization and turnover of Gup1p were revealed by expression of the Gup1p-GFP fusion protein in a set of strains bearing mutations in specific steps of the secretory and endocytic pathways. The chimaerical protein was targeted to the plasma membrane through a Sec6-dependent process; on treatment with glucose, it was endocytosed through END3 and targeted for degradation in the vacuole. Gup1p belongs to the list of yeast proteins rapidly down-regulated by changing the carbon source in the culture medium, in agreement with the concept that post-translational modifications triggered by glucose affect proteins of peripheral functions. The immunoelectron microscopy assays of cells expressing either Gup1-GFP or GFP-Gup1 fusions suggested the Gup1p membrane topology: the N-terminus lies in the periplasmic space, whereas its C-terminal tail has an intracellular location. An extra cytosolic location of the N-terminal tail is not generally predicted or determined in yeast membrane transporters.
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Affiliation(s)
- Gianluca Bleve
- *Istituto di Scienze delle Produzioni Alimentari Sezione di Lecce, CNR, 73100 Lecce, Italy
| | - Giuseppe Zacheo
- *Istituto di Scienze delle Produzioni Alimentari Sezione di Lecce, CNR, 73100 Lecce, Italy
| | - Maria Stella Cappello
- *Istituto di Scienze delle Produzioni Alimentari Sezione di Lecce, CNR, 73100 Lecce, Italy
| | - Franco Dellaglio
- †Dipartimento Scientifico e Tecnologico, Universita’ di Verona, 37134 Verona, Italy
| | - Francesco Grieco
- *Istituto di Scienze delle Produzioni Alimentari Sezione di Lecce, CNR, 73100 Lecce, Italy
- To whom correspondence should be addressed (email )
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Brejning J, Arneborg N, Jespersen L. Identification of genes and proteins induced during the lag and early exponential phase of lager brewing yeasts. J Appl Microbiol 2005; 98:261-71. [PMID: 15659180 DOI: 10.1111/j.1365-2672.2004.02472.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS The aim of the present study is to identify genes and proteins whose expression is induced in lager brewing yeast during the lag phase and early exponential growth. METHODS AND RESULTS Two-dimensional gel electrophoresis was used to identify proteins induced during the lag and early exponential phase of lager brewing yeast in minimal medium. The identified, early-induced proteins were Ade17p, Eno2p, Ilv5gp, Sam1p, Rps21p and Ssa2p. For most of these proteins, the patterns of induction differed from those of the corresponding genes. However, the genes had similar early expression patterns in minimal medium as observed during lager brewing conditions. The expression of previously identified early-induced genes in Saccharomyces cerevisiae grown in minimal medium, ADO1, ALD6, ASC1, ERG4, GPP1, RPL25, SSB1 and YKL056C, was also early induced in lager yeast under brewing conditions. CONCLUSIONS The results indicate that the above-mentioned genes in general are induced during the lag phase and early exponential growth in Saccharomyces yeasts. The processes in which these genes take part are likely to play an important role during growth initiation. SIGNIFICANCE AND IMPACT OF THE STUDY Increased knowledge regarding the early growth phase of lager brewing yeast was obtained. Further, the universality of the identified expression patterns suggests new methodologies for optimization and control of growth initiation during brewing fermentations.
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Affiliation(s)
- J Brejning
- Department of Food Science, Food Microbiology, The Royal Veterinary and Agricultural University, Rolighedsvej, Frederiksberg C, Denmark
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18
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Kobi D, Zugmeyer S, Potier S, Jaquet-Gutfreund L. Two-dimensional protein map of an ?ale?-brewing yeast strain: proteome dynamics during fermentation. FEMS Yeast Res 2004; 5:213-30. [PMID: 15556083 DOI: 10.1016/j.femsyr.2004.07.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2004] [Revised: 06/28/2004] [Accepted: 07/01/2004] [Indexed: 11/28/2022] Open
Abstract
The first protein map of an ale-fermenting yeast is presented in this paper: 205 spots corresponding to 133 different proteins were identified. Comparison of the proteome of this ale strain with a lager brewing yeast and the Saccharomyces cerevisiae strain S288c confirmed that this ale strain is much closer to S288c than the lager strain at the proteome level. The dynamics of the ale-brewing yeast proteome during production-scale fermentation was analysed at the beginning and end of the first and the third usage of the yeast (called generation in the brewing industry). During the first generation, most changes were related to the switch from aerobic propagation to anaerobic fermentation. Fewer changes were observed during the third generation but certain stress-response proteins such as Hsp26p, Ssa4p and Pnc1p exhibited constitutive expression in subsequent generations. The ale brewing yeast strain appears to be quite well adapted to fermentation conditions and stresses.
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Affiliation(s)
- Dominique Kobi
- TEPRAL, Centre de recherche des brasseries Kronenbourg, 68 route d'Oberhausbergen, F-67037 Strasbourg Cedex, France
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19
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Driedzic WR, Ewart KV. Control of glycerol production by rainbow smelt (Osmerus mordax) to provide freeze resistance and allow foraging at low winter temperatures. Comp Biochem Physiol B Biochem Mol Biol 2004; 139:347-57. [PMID: 15544960 DOI: 10.1016/j.cbpc.2004.04.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2003] [Revised: 03/26/2004] [Accepted: 04/04/2004] [Indexed: 11/19/2022]
Abstract
The rainbow smelt (Osmerus mordax) is a small anadromous fish that actively feeds under the ice at temperatures as low as the freeze point of seawater. Freezing is avoided through the production of both non-colligative antifreeze protein (AFP) and glycerol that acts in a colligative manner. Glycerol is constantly lost across the gills and skin, thus glycerol production must continue on a sustained basis at low winter temperatures. AFP begins to accumulate in early fall while water temperatures are still high. Glycerol production is triggered when water temperatures decrease to about 5 degrees C. Glycerol levels rapidly increase with carbon flow from dihydroxyacetone phosphate (DHAP) to glycerol 3-phosphate (G3P) to glycerol. Glucose/glycogen serves as the initial carbon source for glycerol accumulation with amino acids contributing thereafter. The period of glycerol accumulation is associated with increases in GPDH mRNA and PEPCK mRNA followed by elevations in protein synthesis and enzyme activities. Plasma glycerol levels may reach in excess of 500 mM in winter. The high freeze resistance allows rainbow smelt to invade water of low temperature and forage for food. The lower the temperature, the higher the glycerol must be, and the higher the glycerol the greater the loss to the environment through diffusion. During the winter, rainbow smelt feed upon protein rich invertebrates with glycerol production being fueled in part by dietary amino acids via the gluconeogenic pathway. At winter temperatures, glycerol is quantitatively more important than AFP in providing freeze resistance of blood; however, the importance of AFPs to other tissues is yet to be assessed. Glycerol levels rapidly plummet in the spring when water temperature is still close to 0 degrees C. During this period, freeze resistance must be provided by AFP alone. Overall, the phenomenon of glycerol production by rainbow smelt reveals an elegant connection of biochemistry to ecology that allows this species to exploit an otherwise unavailable food resource.
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Affiliation(s)
- William R Driedzic
- Ocean Sciences Centre, Memorial University of Newfoundland, Marine Lab. Drive, St. John's, NL, Canada A1C 5S7.
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20
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Welin J, Wilkins JC, Beighton D, Svensäter G. Protein expression by Streptococcus mutans during initial stage of biofilm formation. Appl Environ Microbiol 2004; 70:3736-41. [PMID: 15184181 PMCID: PMC427790 DOI: 10.1128/aem.70.6.3736-3741.2004] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cells growing on surfaces in biofilms exhibit properties distinct from those of planktonic cells, such as increased resistance to biocides and antimicrobial agents. In spite of increased interest in biofilms, very little is known about alterations in cell physiology that occur upon attachment of cells to a surface. In this study we have investigated the changes induced in the protein synthesis by contact of Streptococcus mutans with a surface. Log-phase planktonic cells of S. mutans were allowed to adhere to a glass slide for 2 h in the presence of a (14)C-amino acid mixture. Nonadhered cells were washed away, and the adhered cells were removed by sonication. The proteins were extracted from the nonadhered planktonic and the adhered biofilm cells and separated by two-dimensional gel electrophoresis followed by autoradiography and image analysis. Image analysis revealed that the relative rate of synthesis of 25 proteins was enhanced and that of 8 proteins was diminished > or =1.3-fold in the biofilm cells. Proteins of interest were identified by mass spectrometry and computer-assisted protein sequence analysis. Of the 33 proteins associated with the adhesion response, all but 10 were identified by mass spectrometry and peptide mass fingerprinting. The most prominent change in adhered cells was the increase in relative synthesis of enzymes involved in carbohydrate catabolism indicating that a redirection in protein synthesis towards energy generation is an early response to contact with and adhesion to a surface.
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Affiliation(s)
- J Welin
- Department of Oral Biology, Faculty of Odontology, Malmö University, SE-205 06 Malmo, Sweden
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21
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Ficarro S, Chertihin O, Westbrook VA, White F, Jayes F, Kalab P, Marto JA, Shabanowitz J, Herr JC, Hunt DF, Visconti PE. Phosphoproteome analysis of capacitated human sperm. Evidence of tyrosine phosphorylation of a kinase-anchoring protein 3 and valosin-containing protein/p97 during capacitation. J Biol Chem 2003; 278:11579-89. [PMID: 12509440 DOI: 10.1074/jbc.m202325200] [Citation(s) in RCA: 394] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Before fertilization can occur, mammalian sperm must undergo capacitation, a process that requires a cyclic AMP-dependent increase in tyrosine phosphorylation. To identify proteins phosphorylated during capacitation, two-dimensional gel analysis coupled to anti-phosphotyrosine immunoblots and tandem mass spectrometry (MS/MS) was performed. Among the protein targets, valosin-containing protein (VCP), a homolog of the SNARE-interacting protein NSF, and two members of the A kinase-anchoring protein (AKAP) family were found to be tyrosine phosphorylated during capacitation. In addition, immobilized metal affinity chromatography was used to investigate phosphorylation sites in whole protein digests from capacitated human sperm. To increase this chromatographic selectivity for phosphopeptides, acidic residues in peptide digests were converted to their respective methyl esters before affinity chromatography. More than 60 phosphorylated sequences were then mapped by MS/MS, including precise sites of tyrosine and serine phosphorylation of the sperm tail proteins AKAP-3 and AKAP-4. Moreover, differential isotopic labeling was developed to quantify phosphorylation changes occurring during capacitation. The phosphopeptide enrichment and quantification methodology coupled to MS/MS, described here for the first time, can be employed to map and compare phosphorylation sites involved in multiple cellular processes. Although we were unable to determine the exact site of phosphorylation of VCP, we did confirm, using a cross-immunoprecipitation approach, that this protein is tyrosine phosphorylated during capacitation. Immunolocalization of VCP showed fluorescent staining in the neck of noncapacitated sperm. However, after capacitation, staining in the neck decreased, and most of the sperm showed fluorescent staining in the anterior head.
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Affiliation(s)
- Scott Ficarro
- Department of Chmeistry, University of Virginia, Charlottesville, Virginia 22908, USA
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22
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Abstract
The ability to adapt to altered availability of free water is a fundamental property of living cells. The principles underlying osmoadaptation are well conserved. The yeast Saccharomyces cerevisiae is an excellent model system with which to study the molecular biology and physiology of osmoadaptation. Upon a shift to high osmolarity, yeast cells rapidly stimulate a mitogen-activated protein (MAP) kinase cascade, the high-osmolarity glycerol (HOG) pathway, which orchestrates part of the transcriptional response. The dynamic operation of the HOG pathway has been well studied, and similar osmosensing pathways exist in other eukaryotes. Protein kinase A, which seems to mediate a response to diverse stress conditions, is also involved in the transcriptional response program. Expression changes after a shift to high osmolarity aim at adjusting metabolism and the production of cellular protectants. Accumulation of the osmolyte glycerol, which is also controlled by altering transmembrane glycerol transport, is of central importance. Upon a shift from high to low osmolarity, yeast cells stimulate a different MAP kinase cascade, the cell integrity pathway. The transcriptional program upon hypo-osmotic shock seems to aim at adjusting cell surface properties. Rapid export of glycerol is an important event in adaptation to low osmolarity. Osmoadaptation, adjustment of cell surface properties, and the control of cell morphogenesis, growth, and proliferation are highly coordinated processes. The Skn7p response regulator may be involved in coordinating these events. An integrated understanding of osmoadaptation requires not only knowledge of the function of many uncharacterized genes but also further insight into the time line of events, their interdependence, their dynamics, and their spatial organization as well as the importance of subtle effects.
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Affiliation(s)
- Stefan Hohmann
- Department of Cell and Molecular Biology/Microbiology, Göteborg University, S-405 30 Göteborg, Sweden.
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Brejning J, Jespersen L. Protein expression during lag phase and growth initiation in Saccharomyces cerevisiae. Int J Food Microbiol 2002; 75:27-38. [PMID: 11999115 DOI: 10.1016/s0168-1605(01)00726-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In order to obtain a better understanding of the biochemical events taking place in Saccharomyces cerevisiae during the lag phase, the proteins expressed during the first hours after inoculation were investigated by two-dimensional (2-D) gel electrophoresis and compared to those expressed in late respiratory growth phase. The studies were performed on a haploid strain (S288C) grown in defined minimal medium. Some of the abundant proteins, whose expression relative to total protein expression was induced during the lag phase, were identified by MALDI MS, and the expression of the corresponding genes was assessed by Northern blotting. The rate of protein synthesis was found to increase strongly during the lag phase and the number of spots detected on 2-D gels increased from 502 spots just after inoculation to 1533 spots at the end of the lag phase. During the first 20 min, the number of detectable spots was considerably reduced compared to the number of spots detected from the yeast in respiratory growth just prior to harvest and inoculation (747 spots), indicating an immediate pausing or shutdown in synthesis of many proteins just after inoculation. In this period, the cells got rid of most of their buds. The MALDI MS-identified, lag phase-induced proteins were adenosine kinase (Ado1p), whose cellular role is presently uncertain, cytosolic acetaldehyde dehydrogenase (Ald6p) and (DL)-glycerol-3-phosphatase 1, both involved in carbohydrate metabolism, a ribosomal protein (Asc1p), a fragment of the 70-kDa heat shock protein Ssb1, and translationally controlled tumour protein homologue (Yk1056cp), all involved in translation, and S-adenosylmethionine synthetase I involved in biosynthesis reactions. The level of mRNA of the corresponding genes was found to increase strongly after inoculation. By pattern matching using previously published 2-D maps of yeast proteins, several other lag phase-induced proteins were identified. These were also proteins involved in carbohydrate metabolism, translation, and biosynthesis reactions. The identified proteins together with other, yet unidentified, lag phase-induced proteins are expected to be important for yeast growth initiation and could be valuable biological markers for yeast performance. Such markers would be highly beneficial in the control and optimisation of industrial fermentations.
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Affiliation(s)
- Jeanette Brejning
- Department of Dairy and Food Science, Food Microbiology, The Royal Veterinary and Agricultural University, Frederiksberg C, Denmark.
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24
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de Nobel H, Lawrie L, Brul S, Klis F, Davis M, Alloush H, Coote P. Parallel and comparative analysis of the proteome and transcriptome of sorbic acid-stressed Saccharomyces cerevisiae. Yeast 2001; 18:1413-28. [PMID: 11746603 DOI: 10.1002/yea.793] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Exposure of Saccharomyces cerevisiae to 0.9 mM sorbic acid at pH 4.5 resulted in the upregulation of 10 proteins; Hsp42, Atp2, Hsp26, Ssa1 or Ssa2, Ssb1 or Ssb2, Ssc1, Ssa4, Ach1, Zwf1 and Tdh1; and the downregulation of three proteins; Ade16, Adh3 and Eno2. In parallel, of 6144 ORFs, 94 (1.53%) showed greater than a 1.4-fold increase in transcript level after exposure to sorbic acid and five of these were increased greater than two-fold; MFA1, AGA2, HSP26, SIP18 and YDR533C. Similarly, of 6144 ORFs, 72 (1.17%) showed greater than a 1.4-fold decrease in transcript level and only one of these, PCK1, was decreased greater than two-fold Functional categories of genes that were induced by sorbic acid stress included cell stress (particularly oxidative stress), transposon function, mating response and energy generation. We found that proteomic analysis yielded distinct information from transcript analysis. Only the upregulation of Hsp26 was detected by both methods. Subsequently, we demonstrated that a deletion mutant of Hsp26 was sensitive to sorbic acid. Thus, the induction of Hsp26, which occurs during adaptation to sorbic acid, confers resistance to the inhibitory effects of this compound.
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Affiliation(s)
- H de Nobel
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 SM Amsterdam, The Netherlands
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25
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Leitch V, Agre P, King LS. Altered ubiquitination and stability of aquaporin-1 in hypertonic stress. Proc Natl Acad Sci U S A 2001; 98:2894-8. [PMID: 11226337 PMCID: PMC30236 DOI: 10.1073/pnas.041616498] [Citation(s) in RCA: 113] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Aquaporin-1 (AQP1) water channel protein expression is increased by hypertonic stress. The contribution of changes in protein stability to hypertonic induction of AQP1 have not been described. Incubation of BALB/c fibroblasts spontaneously expressing AQP1 with proteasome inhibitors increased AQP1 expression, suggesting basal proteasome-dependent degradation of the protein. Degradation by the proteasome is thought to be triggered by polyubiquitination of a target protein. To determine whether AQP1 is ubiquitinated, immunoprecipitation with anti-AQP1 antibodies was performed, and the resultant samples were probed by protein immunoblot for the presence of ubiquitin. Immunoblots demonstrated ubiquitination of AQP1 under control conditions that increased after treatment with proteasome inhibitors (MG132, lactacystin). Exposure of cells to hypertonic medium for as little as 4 h decreased ubiquitination of AQP1, an effect that persisted through 24 h in hypertonic medium. Using metabolic labeling with [(35)S]methionine, the half-life of AQP1 protein under isotonic conditions was found to be <4 h. AQP1 protein half-life was markedly increased by exposure of cells to hypertonic medium. These observations provide evidence that aquaporins are a target for ubiquitination and proteasome-dependent degradation. Additionally, these studies demonstrate that reduced protein ubiquitination and increased protein stability lead to increased levels of AQP1 expression during hypertonic stress.
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Affiliation(s)
- V Leitch
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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26
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Lewis TS, Hunt JB, Aveline LD, Jonscher KR, Louie DF, Yeh JM, Nahreini TS, Resing KA, Ahn NG. Identification of novel MAP kinase pathway signaling targets by functional proteomics and mass spectrometry. Mol Cell 2000; 6:1343-54. [PMID: 11163208 DOI: 10.1016/s1097-2765(00)00132-5] [Citation(s) in RCA: 193] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Functional proteomics provides a powerful method for monitoring global molecular responses following activation of signal transduction pathways, reporting altered protein posttranslational modification and expression. Here we combine functional proteomics with selective activation and inhibition of MKK1/2, in order to identify cellular targets regulated by the MKK/ERK cascade. Twenty-five targets of this signaling pathway were identified, of which only five were previously characterized as MKK/ERK effectors. The remaining targets suggest novel roles for this signaling cascade in cellular processes of nuclear transport, nucleotide excision repair, nucleosome assembly, membrane trafficking, and cytoskeletal regulation. This study represents an application of functional proteomics toward identifying regulated targets of a discrete signal transduction pathway and demonstrates the utility of this discovery-based strategy in elucidating novel MAP kinase pathway effectors.
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Affiliation(s)
- T S Lewis
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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27
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Stochaj U, Rassadi R, Chiu J. Stress-mediated inhibition of the classical nuclear protein import pathway and nuclear accumulation of the small GTPase Gsp1p. FASEB J 2000; 14:2130-2. [PMID: 11024003 DOI: 10.1096/fj.99-0751fje] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Stress modifies all aspects of cellular physiology, including the targeting of macromolecules to the nucleus. To determine how distinct types of stress affect classical nuclear protein import, we followed the distribution of NLS-GFP, a reporter protein containing a classical nuclear localization sequence (NLS) fused to green fluorescent protein GFP. Nuclear accumulation of NLS-GFP requires import to be constitutively active; inhibition of import redistributes NLS-GFP throughout the nucleus and cytoplasm. In the yeast Saccharomyces cerevisiae, starvation, heat shock, ethanol and hydrogen peroxide rapidly inhibited classical nuclear import, whereas osmotic stress had no effect. To define the mechanisms underlying the inhibition of classical nuclear import, we located soluble components of the nuclear transport apparatus. Failure to accumulate NLS-GFP in the nucleus always correlated with a redistribution of the small GTPase Gsp1p. Whereas predominantly nuclear under normal conditions, Gsp1p equilibrated between nucleus and cytoplasm in cells exposed to starvation, heat, ethanol or hydrogen peroxide. Furthermore, analysis of yeast strains carrying mutations in different nuclear transport factors demonstrated a role for NTF2, PRP20 and MOG1 in establishing a Gsp1p gradient, as conditional lethal alleles of NTF2 and PRP20 or a deletion of MOG1 prevented Gsp1p nuclear accumulation. On the basis of these results, we now propose that certain types of stress release Gsp1p from its nuclear anchors, thereby promoting a collapse of the nucleocytoplasmic Gsp1p gradient and inhibiting classical nuclear protein import.
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Affiliation(s)
- U Stochaj
- Department of Physiology, McGill University, Montreal, PQ, Canada, H3G 1Y6.
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28
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Holst B, Lunde C, Lages F, Oliveira R, Lucas C, Kielland-Brandt MC. GUP1 and its close homologue GUP2, encoding multimembrane-spanning proteins involved in active glycerol uptake in Saccharomyces cerevisiae. Mol Microbiol 2000; 37:108-24. [PMID: 10931309 DOI: 10.1046/j.1365-2958.2000.01968.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Many yeast species can utilize glycerol, both as a sole carbon source and as an osmolyte. In Saccharomyces cerevisiae, physiological studies have previously shown the presence of an active uptake system driven by electrogenic proton symport. We have used transposon mutagenesis to isolate mutants affected in the transport of glycerol into the cell. Here we present the identification of YGL084c, encoding a multimembrane-spanning protein, as being essential for proton symport of glycerol into S. cerevisiae. The gene is named GUP1 (glycerol uptake) and, for growth on glycerol, is important as a carbon and energy source. In addition, in strains deficient in glycerol production it also provides osmotic protection by the addition of glycerol. Another open reading frame (ORF), YPL189w, presenting a high degree of homology to YGL084c, similarly appears to be involved in active glycerol uptake in salt-containing glucose-based media in strains deficient in glycerol production. Analogously, this gene is named GUP2. To our knowledge, this is the first report on a gene product involved in active transport of glycerol in yeasts. Mutations with the same phenotypes occurred in two other ORFs of previously unknown function, YDL074c and YPL180w.
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Affiliation(s)
- B Holst
- Department of Yeast Genetics, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Copenhagen Valby, Denmark
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29
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Hoffert JD, Leitch V, Agre P, King LS. Hypertonic induction of aquaporin-5 expression through an ERK-dependent pathway. J Biol Chem 2000; 275:9070-7. [PMID: 10722758 DOI: 10.1074/jbc.275.12.9070] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aquaporin-5 (AQP5) is a water channel protein expressed in lung, salivary gland, and lacrimal gland epithelia. Each of these sites may experience fluctuations in surface liquid osmolarity; however, osmotic regulation of AQP5 expression has not been reported. This study demonstrates that AQP5 is induced by hypertonic stress and that induction requires activation of extracellular signal-regulated kinase (ERK). Incubation of mouse lung epithelial cells (MLE-15) in hypertonic medium produced a dose-dependent increase in AQP5 expression; AQP5 protein peaked by 24 h and returned to baseline levels within hours of returning cells to isotonic medium. AQP5 induction was observed only with relatively impermeable solutes, suggesting an osmotic pressure gradient is required for induction. ERK was selectively activated in MLE-15 cells by hypertonic stress, and inhibition of ERK activation with two distinct mitogen-activated extracellular regulated kinase kinase (MEK) inhibitors, U0126 and PD98059, blocked AQP5 induction. AQP5 induction was also observed in the lung, salivary, and lacrimal glands of hyperosmolar rats, suggesting potential physiologic relevance for osmotic regulation of AQP5 expression. This report provides the first example of hypertonic induction of an extrarenal aquaporin, as well as the first association between mitogen-activated protein kinase signaling and aquaporin expression.
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Affiliation(s)
- J D Hoffert
- Department of Biological Chemistry, Division of Pulmonary and Critical Care Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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30
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Rep M, Krantz M, Thevelein JM, Hohmann S. The transcriptional response of Saccharomyces cerevisiae to osmotic shock. Hot1p and Msn2p/Msn4p are required for the induction of subsets of high osmolarity glycerol pathway-dependent genes. J Biol Chem 2000; 275:8290-300. [PMID: 10722658 DOI: 10.1074/jbc.275.12.8290] [Citation(s) in RCA: 445] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have analyzed the transcriptional response to osmotic shock in the yeast Saccharomyces cerevisiae. The mRNA level of 186 genes increased at least 3-fold after a shift to NaCl or sorbitol, whereas that of more than 100 genes was at least 1.5-fold diminished. Many induced genes encode proteins that presumably contribute to protection against different types of damage or encode enzymes in glycerol, trehalose, and glycogen metabolism. Several genes, which encode poorly expressed isoforms of enzymes in carbohydrate metabolism, were induced. The high osmolarity glycerol (HOG) pathway is required for full induction of many but not all genes. The recently characterized Hot1p transcription factor is required for normal expression of a subset of the HOG pathway-dependent responses. Stimulated expression of the genes that required the general stress-response transcription factors Msn2p and Msn4p was also reduced in a hog1 mutant, suggesting that Msn2p/Msn4p might be regulated by the HOG pathway. The expression of genes that are known to be controlled by the mating pheromone response pathway was stimulated by osmotic shock specifically in a hog1 mutant. Inappropriate activation of the mating response may contribute to the growth defect of a hog1 mutant in high osmolarity medium.
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Affiliation(s)
- M Rep
- Laboratorium voor Moleculaire Celbiologie, Katholieke Universiteit Leuven, Kardinaal Mercierlaan 92, B-3001 Leuven-Heverlee, Flanders, Belgium
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31
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Svensäter G, Sjögreen B, Hamilton IR. Multiple stress responses in Streptococcus mutans and the induction of general and stress-specific proteins. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 1):107-117. [PMID: 10658657 DOI: 10.1099/00221287-146-1-107] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The authors have previously demonstrated that Streptococcus mutans shows an exponential-phase acid-tolerance response following an acid shock from pH 7.5 to 5.5 that enhances survival at pH 3.0. In this study the response of S. mutans H7 to acid shock was compared with the responses generated by salt, heat, oxidation and starvation. Prior induction of the acid-tolerance response did not cross-protect the cells from a subsequent challenge by the other stresses; however, prior adaptation to the other stresses, except heat (42 degrees C), protected the cells during a subsequent acid challenge at pH 3.5. Starvation by fivefold dilution of the basal medium (BM) plus fivefold reduction of its glucose content increased the numbers of survivors 12-fold, whereas elimination of glucose from fivefold-diluted BM led to a sevenfold enhancement compared to the control cells; this indicated a relationship between the acid and starvation responses. The stress responses were further characterized by comparing the 2D electrophoretic protein profiles of exponential-phase cells subjected to the various stress conditions. Cells were grown to exponential phase at pH 7.5 (37 degrees C) and then incubated for 30 min under the various stress conditions in the presence of 14C-labelled amino acids followed by cell extraction, protein separation by 2D gel electrophoresis and image analysis of the resulting autoradiograms. Using consistent twofold or greater changes in IOD % as a measure, oxidative stress resulted in the upregulation of 69 proteins, 15 of which were oxidation-specific, and in the downregulation of 24 proteins, when compared to the control cells. An acid shock from pH 7.5 to 5.5 enhanced synthesis of 64 proteins, 25 of them acid-specific, while 49 proteins exhibited diminished synthesis. The dilution of BM resulted in the increased formation of 58 proteins, with 11 starvation-specific proteins and 20 showing decreased synthesis. Some 52 and 40 proteins were enhanced by salt and heat stress, with 10 and 6 of these proteins, respectively, specific to the stress. The synthesis of a significant number of proteins was increased by more than one, but not all stress conditions; six proteins were enhanced by all five stress conditions and could be classified as general stress proteins. Clearly, the response of S. mutans to adverse environmental conditions results in complex and diverse alterations in protein synthesis to further cell survival.
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Affiliation(s)
- Gunnel Svensäter
- Department of Oral Microbiology, Malmö University, S-21421 Malmö, Sweden1
| | - Bodil Sjögreen
- Department of Oral Microbiology, Malmö University, S-21421 Malmö, Sweden1
| | - Ian R Hamilton
- Department of Oral Biology, University of Manitoba, 780 Bannatyne Ave, Winnipeg, Manitoba, Canada R3E 0W22
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Klipp E, Heinrich R. Competition for enzymes in metabolic pathways: implications for optimal distributions of enzyme concentrations and for the distribution of flux control. Biosystems 1999; 54:1-14. [PMID: 10658833 DOI: 10.1016/s0303-2647(99)00059-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The structures of biochemical pathways are assumed to be determined by evolutionary optimization processes. In the framework of mathematical models, these structures should be explained by the formulation of optimization principles. In the present work, the principle of minimal total enzyme concentration at fixed steady state fluxes is applied to metabolic networks. According to this principle there exists a competition of the reactions for the available amount of enzymes such that all biological functions are maintained. In states which fulfil these optimization criteria the enzyme concentrations are distributed in a non-uniform manner among the reactions. This result has consequences for the distribution of flux control. It is shown that the flux control matrix c, the elasticity matrix epsilon, and the vector e of enzyme concentrations fulfil in optimal states the relations c(T)e = e and epsilon(T)e = 0. Starting from a well-balanced distribution of enzymes the minimization of total enzyme concentration leads to a lowering of the SD of the flux control coefficients.
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Affiliation(s)
- E Klipp
- Humboldt University Berlin, Institute of Biology, Theoretical Biophysics, Germany. edda=
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Perrot M, Sagliocco F, Mini T, Monribot C, Schneider U, Shevchenko A, Mann M, Jenö P, Boucherie H. Two-dimensional gel protein database of Saccharomyces cerevisiae (update 1999). Electrophoresis 1999; 20:2280-98. [PMID: 10493132 DOI: 10.1002/(sici)1522-2683(19990801)20:11<2280::aid-elps2280>3.0.co;2-q] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
By proving the opportunity to visualize several hundred proteins at a time, two-dimensional (2-D) gel electrophoresis is an important tool for proteome research. In order to take advantage of the full potential of this technique for yeast studies, we have undertaken a systematic identification of yeast proteins resolved by this technique. We report here the identification of 92 novel protein spots on the yeast 2-D protein map. These identifications extend the number of protein spots identified on our yeast reference map to 401. These spots correspond to the products of 279 different genes. They have been essentially identified by three methods: gene overexpression, amino acid composition and mass spectrometry. These data can be accessed on the Yeast Protein Map server (htpp://www.ibgc.u-bordeaux2.fr/YPM).
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Affiliation(s)
- M Perrot
- Institut de Biochimie et Génétique Cellulaires, UPR CNRS 9026, Bordeaux, France
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Resing KA, Ahn NG. Applications of mass spectrometry to signal transduction. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1999; 71:501-23. [PMID: 10354711 DOI: 10.1016/s0079-6107(98)00048-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Advances in mass spectrometry instrumentation, protocols for sample handling, and computational methods provide powerful new approaches to solving problems in analytical biochemistry. This review summarizes recent work illustrating ways in which mass spectrometry has been used to address questions relevant to signal transduction. Rather than encompass all of the instruments or methodologies that might be brought to bear on these problems, we present an overview of commonly used techniques, promising new methodologies, and some applications.
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Affiliation(s)
- K A Resing
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309, USA
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Nau-Wagner G, Boch J, Le Good JA, Bremer E. High-affinity transport of choline-O-sulfate and its use as a compatible solute in Bacillus subtilis. Appl Environ Microbiol 1999; 65:560-8. [PMID: 9925583 PMCID: PMC91062 DOI: 10.1128/aem.65.2.560-568.1999] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/1998] [Accepted: 11/10/1998] [Indexed: 11/20/2022] Open
Abstract
We report here that the naturally occurring choline ester choline-O-sulfate serves as an effective compatible solute for Bacillus subtilis, and we have identified a high-affinity ATP-binding cassette (ABC) transport system responsible for its uptake. The osmoprotective effect of this trimethylammonium compound closely matches that of the potent and widely employed osmoprotectant glycine betaine. Growth experiments with a set of B. subtilis strains carrying defined mutations in the glycine betaine uptake systems OpuA, OpuC, and OpuD and in the high-affinity choline transporter OpuB revealed that choline-O-sulfate was specifically acquired from the environment via OpuC. Competition experiments demonstrated that choline-O-sulfate functioned as an effective competitive inhibitor for OpuC-mediated glycine betaine uptake, with a Ki of approximately 4 microM. Uptake studies with [1, 2-dimethyl-14C]choline-O-sulfate showed that its transport was stimulated by high osmolality, and kinetic analysis revealed that OpuC has high affinity for choline-O-sulfate, with a Km value of 4 +/- 1 microM and a maximum rate of transport (Vmax) of 54 +/- 3 nmol/min. mg of protein in cells grown in minimal medium with 0.4 M NaCl. Growth studies utilizing a B. subtilis mutant defective in the choline to glycine betaine synthesis pathway and natural abundance 13C nuclear magnetic resonance spectroscopy of whole-cell extracts from the wild-type strain demonstrated that choline-O-sulfate was accumulated in the cytoplasm and was not hydrolyzed to choline by B. subtilis. In contrast, the osmoprotective effect of acetylcholine for B. subtilis is dependent on its biotransformation into glycine betaine. Choline-O-sulfate was not used as the sole carbon, nitrogen, or sulfur source, and our findings thus characterize this choline ester as an effective compatible solute and metabolically inert stress compound for B. subtilis. OpuC mediates the efficient transport not only of glycine betaine and choline-O-sulfate but also of carnitine, crotonobetaine, and gamma-butyrobetaine (R. Kappes and E. Bremer, Microbiology 144:83-90, 1998). Thus, our data underscore its crucial role in the acquisition of a variety of osmoprotectants from the environment by B. subtilis.
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Affiliation(s)
- G Nau-Wagner
- Philipps University Marburg, Department of Biology, D-35032 Marburg, Federal Republic of Germany
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Gustin MC, Albertyn J, Alexander M, Davenport K. MAP kinase pathways in the yeast Saccharomyces cerevisiae. Microbiol Mol Biol Rev 1998; 62:1264-300. [PMID: 9841672 PMCID: PMC98946 DOI: 10.1128/mmbr.62.4.1264-1300.1998] [Citation(s) in RCA: 703] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A cascade of three protein kinases known as a mitogen-activated protein kinase (MAPK) cascade is commonly found as part of the signaling pathways in eukaryotic cells. Almost two decades of genetic and biochemical experimentation plus the recently completed DNA sequence of the Saccharomyces cerevisiae genome have revealed just five functionally distinct MAPK cascades in this yeast. Sexual conjugation, cell growth, and adaptation to stress, for example, all require MAPK-mediated cellular responses. A primary function of these cascades appears to be the regulation of gene expression in response to extracellular signals or as part of specific developmental processes. In addition, the MAPK cascades often appear to regulate the cell cycle and vice versa. Despite the success of the gene hunter era in revealing these pathways, there are still many significant gaps in our knowledge of the molecular mechanisms for activation of these cascades and how the cascades regulate cell function. For example, comparison of different yeast signaling pathways reveals a surprising variety of different types of upstream signaling proteins that function to activate a MAPK cascade, yet how the upstream proteins actually activate the cascade remains unclear. We also know that the yeast MAPK pathways regulate each other and interact with other signaling pathways to produce a coordinated pattern of gene expression, but the molecular mechanisms of this cross talk are poorly understood. This review is therefore an attempt to present the current knowledge of MAPK pathways in yeast and some directions for future research in this area.
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Affiliation(s)
- M C Gustin
- Department of Biochemistry and Cell Biology Rice University, Houston, Texas 77251-1892, USA.
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37
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Stress responses ofBacillus subtilis to high osmolarity environments: Uptake and synthesis of osmoprotectants. J Biosci 1998. [DOI: 10.1007/bf02936138] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Spiegelhalter F, Bremer E. Osmoregulation of the opuE proline transport gene from Bacillus subtilis: contributions of the sigma A- and sigma B-dependent stress-responsive promoters. Mol Microbiol 1998; 29:285-96. [PMID: 9701821 DOI: 10.1046/j.1365-2958.1998.00929.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The opuE gene from Bacillus subtilis encodes a transport system (OpuE) for osmoprotective proline uptake and is expressed from two osmoregulated promoters: opuE P-1 recognized by the vegetative sigma factor A (sigma A and opuE P-2 dependent on the stress-induced transcription factor sigma B (sigma B). The contributions of these two promoters to osmoregulation of opuE were analysed. Genetic studies using chromosomal opuE-treA operon fusions revealed that opuE transcription is rapidly induced after an osmotic upshock. The strength of opuE expression is proportionally linked to the osmolarity of the growth medium. Deletion analysis of the opuE regulatory region identified a 330 bp DNA segment carrying all sequences required in cis for full and osmoregulated transcription. The proper rotational orientation of the upstream region present within this fragment was essential for the function of both opuE promoters. Mutant opuE-treA fusions with defects in either the sigma A-or the sigma B-dependent promoters revealed different contributions of these sequences to the overall osmoregulation of opuE. opuE P-2 (sigma B) activity increased transiently after an osmotic upshock and did not significantly contribute to the level of opuE expression in cells subjected to long-term osmotic stress. In contrast, transcription initiating from opuE P-1 (sigma A) rose in proportion to the external osmolarity and was maintained at high levels. Moreover, both promoters exhibited a different response to the osmoprotectant glycine betaine in the medium. Our results suggest that at least two different signal transduction pathways operate in B. subtilis to communicate osmotic changes in the environment to the transcription apparatus of the cell.
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Nawrocki A, Larsen MR, Podtelejnikov AV, Jensen ON, Mann M, Roepstorff P, Görg A, Fey SJ, Larsen PM. Correlation of acidic and basic carrier ampholyte and immobilized pH gradient two-dimensional gel electrophoresis patterns based on mass spectrometric protein identification. Electrophoresis 1998; 19:1024-35. [PMID: 9638949 DOI: 10.1002/elps.1150190618] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Separation of proteins on either carrier ampholyte-based or immobilized pH gradient-based two-dimensional (2-D) gels gives rise to electrophoretic patterns that are difficult to compare visually. In this paper we have used matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to determine the identities of 335 protein spots in these two 2-D gel systems, including a substantial number of basic proteins which had never been identified before. Proteins that were identified in both gel systems allowed us to cross-reference the gel patterns. Vector analysis of these cross-references demonstrated that there is no obvious pattern by which the mobility of a protein in one gel system can be used to predict its mobility in the other. Thus, as laboratories adopt the immobilized pH gradient-based 2-D gel systems, the only reliable means of translating the data gained with the carrier ampholyte-based gel system is to positively identify the proteins in both 2-D systems.
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Affiliation(s)
- A Nawrocki
- Center for Proteome Analysis in Life Sciences, International Science Park Odense, Denmark
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Humphery-Smith I, Cordwell SJ, Blackstock WP. Proteome research: complementarity and limitations with respect to the RNA and DNA worlds. Electrophoresis 1997; 18:1217-42. [PMID: 9298643 DOI: 10.1002/elps.1150180804] [Citation(s) in RCA: 164] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A methodological overview of proteome analysis is provided along with details of efforts to achieve high-throughput screening (HTS) of protein samples derived from two-dimensional electrophoresis gels. For both previously sequenced organisms and those lacking significant DNA sequence information, mass spectrometry has a key role to play in achieving HTS. Prototype robotics designed to conduct appropriate chemistries and deliver 700-1000 protein (genes) per day to batteries of mass spectrometers or liquid chromatography (LC)-based analyses are well advanced, as are efforts to produce high density gridded arrays containing > 1000 proteins on a single matrix assisted laser desorption ionisation/time-of-flight (MALDI-TOF) sample stage. High sensitivity HTS of proteins is proposed by employing principally mass spectrometry in an hierarchical manner: (i) MALDI-TOF-mass spectrometry (MS) on at least 1000 proteins per day; (ii) electrospray ionisation (ESI)/MS/MS for analysis of peptides with respect to predicted fragmentation patterns or by sequence tagging; and (iii) ESI/MS/MS for peptide sequencing. Genomic sequences when complemented with information derived from hybridisation assays and proteome analysis may herald in a new era of holistic cellular biology. The current preoccupation with the absolute quantity of gene-product (RNA and/or protein) should move backstage with respect to more molecularly relevant parameters, such as: molecular half-life; synthesis rate; functional competence (presence or absence of mutations); reaction kinetics; the influence of individual gene-products on biochemical flux; the influence of the environment, cell-cycle, stress and disease on gene-products; and the collective roles of multigenic and epigenetic phenomena governing cellular processes. Proteome analysis is demonstrated as being capable of proceeding independently of DNA sequence information and aiding in genomic annotation. Its ability to confirm the existence of gene-products predicted from DNA sequence is a major contribution to genomic science. The workings of software engines necessary to achieve large-scale proteome analysis are outlined, along with trends towards miniaturisation, analyte concentration and protein detection independent of staining technologies. A challenge for proteome analysis into the future will be to reduce its dependence on two-dimensional (2-D) gel electrophoresis as the preferred method of separating complex mixtures of cellular proteins. Nonetheless, proteome analysis already represents a means of efficiently complementing differential display, high density expression arrays, expressed sequence tags, direct or subtractive hybridisation, chromosomal linkage studies and nucleic acid sequencing as a problem solving tool in molecular biology.
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Affiliation(s)
- I Humphery-Smith
- University of Sydney, Centre for Proteome Research and Gene-Product Mapping, National Innovation Centre, Eveleigh, Australia.
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