1
|
Guo H, Lu F, Lu R, Huang M, Li X, Yuan J, Wang F. A novel tumor 4-driver gene signature for the prognosis of hepatocellular carcinoma. Heliyon 2023; 9:e17054. [PMID: 37484410 PMCID: PMC10361245 DOI: 10.1016/j.heliyon.2023.e17054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/02/2023] [Accepted: 06/06/2023] [Indexed: 07/25/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC), the main type of liver cancer, is the second most lethal tumor worldwide, with a 5-year survival rate of only 18%. Driver genes facilitate cancer cell growth and spread in the tumor microenvironment. Here, a comprehensive driver gene signature for the prognosis of HCC was developed. Methods HCC driver genes were analyzed comprehensively to develop a better prognostic signature. The dataset of HCC patients included mRNA sequencing data and clinical information from the TCGA, the ICGC, and the Guangxi Medical University Cancer Hospital cohorts. First, LASSO was performed to develop a prognostic signature for differentially expressed driver genes in the TCGA cohort. Then, the robustness of the signature was assessed using survival and time-dependent ROC curves. Furthermore, independent predictors were determined using univariate and multivariate Cox regression analyses. Stepwise multi-Cox regression analysis was employed to identify significant variables for the construction of a nomogram that predicts survival rates. Functional analysis by Spearman correlation analysis, enrichment analysis (GO, KEGG, and GSEA), and immunoassay (ssGSEA and xCell) were performed. Result A 4-driver gene signature (CLTC, DNMT3A, GMPS, and NRAS) was successfully constructed and showed excellent predictive efficiency in three cohorts. The nomogram indicated high predictive accuracy for the 1-, 3-, and 5-year prognoses of HCC patients, which included clinical information and risk score. Enrichment analysis revealed that driver genes were involved in regulating oncogenic processes, including the cell cycle and metabolic pathways, which were associated with the progression of HCC. ssGSEA and xCell showed differences in immune infiltration and the immune microenvironment between the two risk groups. Conclusion The 4-driver gene signature is closely associated with the survival prediction of HCC and is expected to provide new insights into targeted therapy for HCC patients.
Collapse
Affiliation(s)
- Houtian Guo
- First Clinical College of Guangxi Medical University, Nanning, China
| | - Fei Lu
- First Clinical College of Guangxi Medical University, Nanning, China
| | - Rongqi Lu
- First Clinical College of Guangxi Medical University, Nanning, China
| | - Meiqi Huang
- First Clinical College of Guangxi Medical University, Nanning, China
| | - Xuejing Li
- Department of Physiology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Jianhui Yuan
- Department of Physics, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Feng Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
- Key Laboratory of Biological Molecular Medicine Research, Guangxi Medical University, Education Department of Guangxi Zhuang Autonomous Region, Nanning, China
| |
Collapse
|
2
|
Kershaw CJ, Jennings MD, Cortopassi F, Guaita M, Al-Ghafli H, Pavitt GD. GTP binding to translation factor eIF2B stimulates its guanine nucleotide exchange activity. iScience 2021; 24:103454. [PMID: 34877508 PMCID: PMC8633983 DOI: 10.1016/j.isci.2021.103454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/26/2021] [Accepted: 11/11/2021] [Indexed: 01/23/2023] Open
Abstract
eIF2B is the guanine nucleotide exchange factor (GEF) required for cytoplasmic protein synthesis initiation in eukaryotes and its regulation within the integrated stress response (ISR). It activates its partner factor eIF2, thereby promoting translation initiation. Here we provide evidence through biochemical and genetic approaches that eIF2B can bind directly to GTP and this can enhance its rate of GEF activity toward eIF2–GDP in vitro. GTP binds to a subcomplex of the eIF2Bγ and ε subunits. The eIF2Bγ amino-terminal domain shares structural homology with hexose sugar phosphate pyrophosphorylase enzymes that bind specific nucleotides. A K66R mutation in eIF2Bγ is especially sensitive to guanine or GTP in a range of functional assays. Taken together, our data suggest eIF2Bγ may act as a sensor of purine nucleotide availability and thus modulate eIF2B activity and protein synthesis in response to fluctuations in cellular nucleotide levels. eIF2B, the GDP exchange factor for eIF2 in translation and its control, binds GTP GTP binding enhances the rate of eIF2B GEF activity toward eIF2–GDP in vitro A K66R mutation in yeast eIF2Bγ is sensitive to guanine in vivo or GTP in vitro eIF2B may act as a sensor of purine nucleotide availability
Collapse
Affiliation(s)
- Christopher J Kershaw
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Martin D Jennings
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Francesco Cortopassi
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Margherita Guaita
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Hawra Al-Ghafli
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Graham D Pavitt
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| |
Collapse
|
3
|
Difference in the metabolome of colostrum from healthy mothers and mothers with type 2 diabetic mellitus. Eur Food Res Technol 2021. [DOI: 10.1007/s00217-021-03814-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
4
|
Luzarowski M, Vicente R, Kiselev A, Wagner M, Schlossarek D, Erban A, de Souza LP, Childs D, Wojciechowska I, Luzarowska U, Górka M, Sokołowska EM, Kosmacz M, Moreno JC, Brzezińska A, Vegesna B, Kopka J, Fernie AR, Willmitzer L, Ewald JC, Skirycz A. Global mapping of protein-metabolite interactions in Saccharomyces cerevisiae reveals that Ser-Leu dipeptide regulates phosphoglycerate kinase activity. Commun Biol 2021; 4:181. [PMID: 33568709 PMCID: PMC7876005 DOI: 10.1038/s42003-021-01684-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/08/2021] [Indexed: 01/30/2023] Open
Abstract
Protein-metabolite interactions are of crucial importance for all cellular processes but remain understudied. Here, we applied a biochemical approach named PROMIS, to address the complexity of the protein-small molecule interactome in the model yeast Saccharomyces cerevisiae. By doing so, we provide a unique dataset, which can be queried for interactions between 74 small molecules and 3982 proteins using a user-friendly interface available at https://promis.mpimp-golm.mpg.de/yeastpmi/ . By interpolating PROMIS with the list of predicted protein-metabolite interactions, we provided experimental validation for 225 binding events. Remarkably, of the 74 small molecules co-eluting with proteins, 36 were proteogenic dipeptides. Targeted analysis of a representative dipeptide, Ser-Leu, revealed numerous protein interactors comprising chaperones, proteasomal subunits, and metabolic enzymes. We could further demonstrate that Ser-Leu binding increases activity of a glycolytic enzyme phosphoglycerate kinase (Pgk1). Consistent with the binding analysis, Ser-Leu supplementation leads to the acute metabolic changes and delays timing of a diauxic shift. Supported by the dipeptide accumulation analysis our work attests to the role of Ser-Leu as a metabolic regulator at the interface of protein degradation and central metabolism.
Collapse
Affiliation(s)
- Marcin Luzarowski
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Rubén Vicente
- grid.418390.70000 0004 0491 976XDepartment of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Andrei Kiselev
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany ,grid.503344.50000 0004 0445 6769Laboratoire de Recherche en Sciences Végétales (LRSV), UPS/CNRS, UMR, Castanet Tolosan, France
| | - Mateusz Wagner
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany ,grid.8505.80000 0001 1010 5103University of Wrocław, Faculty of Biotechnology, Laboratory of Medical Biology, Wrocław, Poland
| | - Dennis Schlossarek
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Alexander Erban
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Leonardo Perez de Souza
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Dorothee Childs
- grid.4709.a0000 0004 0495 846XDepartment of Genome Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Izabela Wojciechowska
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Urszula Luzarowska
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany ,grid.7489.20000 0004 1937 0511Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michał Górka
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Ewelina M. Sokołowska
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Monika Kosmacz
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany ,grid.45672.320000 0001 1926 5090Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Juan C. Moreno
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany ,grid.45672.320000 0001 1926 5090Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Aleksandra Brzezińska
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Bhavana Vegesna
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Joachim Kopka
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Alisdair R. Fernie
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Lothar Willmitzer
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Jennifer C. Ewald
- grid.10392.390000 0001 2190 1447Interfaculty Institute of Cell Biology, Eberhard Karls University of Tuebingen, Tuebingen, Germany
| | - Aleksandra Skirycz
- grid.418390.70000 0004 0491 976XDepartment of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany ,grid.5386.8000000041936877XBoyce Thompson Institute, Ithaca, NY USA
| |
Collapse
|
5
|
Oxidative Stress Responses and Nutrient Starvation in MCHM Treated Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2020; 10:4665-4678. [PMID: 33109726 PMCID: PMC7718757 DOI: 10.1534/g3.120.401661] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In 2014, the coal cleaning chemical 4-methylcyclohexane methanol (MCHM) spilled into the water supply for 300,000 West Virginians. Initial toxicology tests showed relatively mild results, but the underlying effects on cellular biology were underexplored. Treated wildtype yeast cells grew poorly, but there was only a small decrease in cell viability. Cell cycle analysis revealed an absence of cells in S phase within thirty minutes of treatment. Cells accumulated in G1 over a six-hour time course, indicating arrest instead of death. A genetic screen of the haploid knockout collection revealed 329 high confidence genes required for optimal growth in MCHM. These genes encode three major cell processes: mitochondrial gene expression/translation, the vacuolar ATPase, and aromatic amino acid biosynthesis. The transcriptome showed an upregulation of pleiotropic drug response genes and amino acid biosynthetic genes and downregulation in ribosome biosynthesis. Analysis of these datasets pointed to environmental stress response activation upon treatment. Overlap in datasets included the aromatic amino acid genes ARO1, ARO3, and four of the five TRP genes. This implicated nutrient deprivation as the signal for stress response. Excess supplementation of nutrients and amino acids did not improve growth on MCHM, so the source of nutrient deprivation signal is still unclear. Reactive oxygen species and DNA damage were directly detected with MCHM treatment, but timepoints showed these accumulated slower than cells arrested. We propose that wildtype cells arrest from nutrient deprivation and survive, accumulating oxidative damage through the implementation of robust environmental stress responses.
Collapse
|
6
|
Saint-Marc C, Ceschin J, Almyre C, Pinson B, Daignan-Fornier B. Genetic investigation of purine nucleotide imbalance in Saccharomyces cerevisiae. Curr Genet 2020; 66:1163-1177. [PMID: 32780163 DOI: 10.1007/s00294-020-01101-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/21/2020] [Accepted: 08/06/2020] [Indexed: 11/28/2022]
Abstract
Because metabolism is a complex balanced process involving multiple enzymes, understanding how organisms compensate for transient or permanent metabolic imbalance is a challenging task that can be more easily achieved in simpler unicellular organisms. The metabolic balance results not only from the combination of individual enzymatic properties, regulation of enzyme abundance, but also from the architecture of the metabolic network offering multiple interconversion alternatives. Although metabolic networks are generally highly resilient to perturbations, metabolic imbalance resulting from enzymatic defect and specific environmental conditions can be designed experimentally and studied. Starting with a double amd1 aah1 mutant that severely and conditionally affects yeast growth, we carefully characterized the metabolic shuffle associated with this defect. We established that the GTP decrease resulting in an adenylic/guanylic nucleotide imbalance was responsible for the growth defect. Identification of several gene dosage suppressors revealed that TAT1, encoding an amino acid transporter, is a robust suppressor of the amd1 aah1 growth defect. We show that TAT1 suppression occurs through replenishment of the GTP pool in a process requiring the histidine biosynthesis pathway. Importantly, we establish that a tat1 mutant exhibits synthetic sickness when combined with an amd1 mutant and that both components of this synthetic phenotype can be suppressed by specific gene dosage suppressors. Together our data point to a strong phenotypic connection between amino acid uptake and GTP synthesis, a connection that could open perspectives for future treatment of related human defects, previously reported as etiologically highly conserved.
Collapse
Affiliation(s)
- Christelle Saint-Marc
- IBGC, UMR 5095, Université de Bordeaux, Bordeaux, France.,Centre National de la Recherche Scientifique IBGC, UMR 5095, Bordeaux, France
| | - Johanna Ceschin
- IBGC, UMR 5095, Université de Bordeaux, Bordeaux, France.,Centre National de la Recherche Scientifique IBGC, UMR 5095, Bordeaux, France
| | - Claire Almyre
- IBGC, UMR 5095, Université de Bordeaux, Bordeaux, France.,Centre National de la Recherche Scientifique IBGC, UMR 5095, Bordeaux, France
| | - Benoît Pinson
- IBGC, UMR 5095, Université de Bordeaux, Bordeaux, France.,Centre National de la Recherche Scientifique IBGC, UMR 5095, Bordeaux, France
| | - Bertrand Daignan-Fornier
- IBGC, UMR 5095, Université de Bordeaux, Bordeaux, France. .,Centre National de la Recherche Scientifique IBGC, UMR 5095, Bordeaux, France.
| |
Collapse
|
7
|
Interactions of GMP with Human Glrx3 and with Saccharomyces cerevisiae Grx3 and Grx4 Converge in the Regulation of the Gcn2 Pathway. Appl Environ Microbiol 2020; 86:AEM.00221-20. [PMID: 32414791 DOI: 10.1128/aem.00221-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/24/2020] [Indexed: 11/20/2022] Open
Abstract
The human monothiol glutaredoxin Glrx3 (PICOT) is ubiquitously distributed in cytoplasm and nuclei in mammalian cells. Its overexpression has been associated with the development of several types of tumors, whereas its deficiency might cause retardation in embryogenesis. Its exact biological role has not been well resolved, although a function as a chaperone distributing iron/sulfur clusters is currently accepted. Yeast humanization and the use of a mouse library have allowed us to find a new partner for PICOT: the human GMP synthase (hGMPs). Both proteins carry out collaborative functions regarding the downregulation of the Saccharomyces cerevisiae Gcn2 pathway under conditions of nutritional stress. Glrx3/hGMPs interact through conserved residues that bridge iron/sulfur clusters and glutathione. This mechanism is also conserved in budding yeast, whose proteins Grx3/Grx4, along with GUA1 (S. cerevisiae GMPs), also downregulate the integrated stress response (ISR) pathway. The heterologous expression of Glrx3/hGMPs efficiently complements Grx3/Grx4. Moreover, the heterologous expression of Glrx3 efficiently complements the novel participation in chronological life span that has been characterized for both Grx3 and Grx4. Our results underscore that the Glrx3/Grx3/Grx4 family presents an evolutionary and functional conservation in signaling events that is partly related to GMP function and contributes to cell life extension.IMPORTANCE Saccharomyces cerevisiae is an optimal eukaryotic microbial model to study biological processes in higher organisms despite the divergence in evolution. The molecular function of yeast glutaredoxins Grx3 and Grx4 is enormously interesting, since both proteins are required to maintain correct iron homeostasis and an efficient response to oxidative stress. The human orthologous Glrx3 (PICOT) is involved in a number of human diseases, including cancer. Our research expanded its utility to human cells. Yeast has allowed the characterization of GMP synthase as a new interacting partner for Glrx3 and also for yeast Grx3 and Grx4, the complex monothiol glutaredoxins/GMPs that participate in the downregulation of the activity of the Gcn2 stress pathway. This mechanism is conserved in yeast and humans. Here, we also show that this family of glutaredoxins, Grx3/Grx4/Glrx3, also has a function related to life extension.
Collapse
|
8
|
Decio P, Ustaoglu P, Roat TC, Malaspina O, Devaud JM, Stöger R, Soller M. Acute thiamethoxam toxicity in honeybees is not enhanced by common fungicide and herbicide and lacks stress-induced changes in mRNA splicing. Sci Rep 2019; 9:19196. [PMID: 31844097 PMCID: PMC6915785 DOI: 10.1038/s41598-019-55534-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/20/2019] [Indexed: 12/19/2022] Open
Abstract
Securing food supply for a growing population is a major challenge and heavily relies on the use of agrochemicals to maximize crop yield. It is increasingly recognized, that some neonicotinoid insecticides have a negative impact on non-target organisms, including important pollinators such as the European honeybee Apis mellifera. Toxicity of neonicotinoids may be enhanced through simultaneous exposure with additional pesticides, which could help explain, in part, the global decline of honeybee colonies. Here we examined whether exposure effects of the neonicotinoid thiamethoxam on bee viability are enhanced by the commonly used fungicide carbendazim and the herbicide glyphosate. We also analysed alternative splicing changes upon pesticide exposure in the honeybee. In particular, we examined transcripts of three genes: (i) the stress sensor gene X box binding protein-1 (Xbp1), (ii) the Down Syndrome Cell Adhesion Molecule (Dscam) gene and iii) the embryonic lethal/abnormal visual system (elav) gene, which are important for neuronal function. Our results showed that acute thiamethoxam exposure is not enhanced by carbendazim, nor glyphosate. Toxicity of the compounds did not trigger stress-induced, alternative splicing in the analysed mRNAs, thereby leaving dormant a cellular response pathway to these man-made environmental perturbations.
Collapse
Affiliation(s)
- Pâmela Decio
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Centro de Estudos de Insetos Sociais, Rio Claro, São Paulo, Brazil
| | - Pinar Ustaoglu
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, and Department of Life Sciences, Imperial College London, Ground Floor, Flowers Building, South Kensington Campus, London, SW7 2AZ, UK
| | - Thaisa C Roat
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Centro de Estudos de Insetos Sociais, Rio Claro, São Paulo, Brazil
| | - Osmar Malaspina
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Centro de Estudos de Insetos Sociais, Rio Claro, São Paulo, Brazil
| | - Jean-Marc Devaud
- Research Center on Animal Cognition, Center for Integrative Biology, Toulouse University, CNRS, UPS, Toulouse, France
| | - Reinhard Stöger
- School of Biosciences, University of Nottingham, LE12 5RD, Nottingham/Sutton Bonington Campus, United Kingdom.
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom.
| |
Collapse
|
9
|
Determination of the Global Pattern of Gene Expression in Yeast Cells by Intracellular Levels of Guanine Nucleotides. mBio 2019; 10:mBio.02500-18. [PMID: 30670615 PMCID: PMC6343037 DOI: 10.1128/mbio.02500-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
This paper investigates whether, independently of the supply of any specific nutrient, gene transcription responds to the energy status of the cell by monitoring ATP and GTP levels. Short pathways for the inducible and futile consumption of ATP or GTP were engineered into the yeast Saccharomyces cerevisiae, and the effect of an increased demand for these purine nucleotides on gene transcription was analyzed. The resulting changes in transcription were most consistently associated with changes in GTP and GEC levels, although the reprogramming in gene expression during glucose repression is sensitive to adenine nucleotide levels. The results show that GTP levels play a central role in determining how genes act to respond to changes in energy supply and that any comprehensive understanding of the control of eukaryotic gene expression requires the elucidation of how changes in guanine nucleotide abundance are sensed and transduced to alter the global pattern of transcription. Correlations between gene transcription and the abundance of high-energy purine nucleotides in Saccharomyces cerevisiae have often been noted. However, there has been no systematic investigation of this phenomenon in the absence of confounding factors such as nutrient status and growth rate, and there is little hard evidence for a causal relationship. Whether transcription is fundamentally responsive to prevailing cellular energetic conditions via sensing of intracellular purine nucleotides, independently of specific nutrition, remains an important question. The controlled nutritional environment of chemostat culture revealed a strong correlation between ATP and GTP abundance and the transcription of genes required for growth. Short pathways for the inducible and futile consumption of ATP or GTP were engineered into S. cerevisiae, permitting analysis of the transcriptional effect of an increased demand for these nucleotides. During steady-state growth using the fermentable carbon source glucose, the futile consumption of ATP led to a decrease in intracellular ATP concentration but an increase in GTP and the guanylate energy charge (GEC). Expression of transcripts encoding proteins involved in ribosome biogenesis, and those controlled by promoters subject to SWI/SNF-dependent chromatin remodelling, was correlated with these nucleotide pool changes. Similar nucleotide abundance changes were observed using a nonfermentable carbon source, but an effect on the growth-associated transcriptional programme was absent. Induction of the GTP-cycling pathway had only marginal effects on nucleotide abundance and gene transcription. The transcriptional response of respiring cells to glucose was dampened in chemostats induced for ATP cycling, but not GTP cycling, and this was primarily associated with altered adenine nucleotide levels.
Collapse
|
10
|
Matsuda S, Kasahara T. Simultaneous and absolute quantification of nucleoside triphosphates using liquid chromatography-triple quadrupole tandem mass spectrometry. Genes Environ 2018; 40:13. [PMID: 30069278 PMCID: PMC6065067 DOI: 10.1186/s41021-018-0101-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 05/23/2018] [Indexed: 11/10/2022] Open
Abstract
Background Nucleoside triphosphates participate in fundamental cellular processes as building blocks of DNA and RNA, energy carriers, and cofactors in enzymatic reactions, and their balance is tightly regulated. Here, we established a simultaneous and absolute quantification method for eight nucleoside triphosphates using liquid chromatography–triple quadrupole tandem mass spectrometry and hydrophilic interaction chromatography. Our method was successfully applied to the extract of human acute myeloid leukemia Molm-13 cells. Results Levels of ribonucleoside triphosphates (2.07 × 108–2.29 × 109 molecules/cell) in Molm-13 cells were two orders of magnitude higher than those of deoxyribonucleoside triphosphates (1.72 × 106–1.40 × 107 molecules/cell). Exposure of Molm-13 cells for 24 h to thymidine, a nucleotide imbalance inducer, increased the levels of cellular dTTP, dGTP, and dATP and decreased only dCTP, resulting in significant inhibition of cell proliferation. Conclusion Our quantification method for nucleoside triphosphates revealed the quantitative relationship between the arrest of cell proliferation and the imbalance of nucleoside triphosphates in thymidine-treated Molm-13 cells. Owing to the short run time (15 min/run), broad adaptability, and throughput performance, we believe that our method is a powerful tool for not only genetic and molecular biology research but also for studying the mechanism of genotoxic compounds and anti-cancer or anti-virus drugs, drug screening, clinical studies, and other fields.
Collapse
Affiliation(s)
- Shun Matsuda
- Safety Evaluation Center, Ecology & Quality Management Division, CSR Division, FUJIFILM Corporation, 210 Nakanuma, Minamiashigara, Kanagawa 250-0193 Japan
| | - Toshihiko Kasahara
- Safety Evaluation Center, Ecology & Quality Management Division, CSR Division, FUJIFILM Corporation, 210 Nakanuma, Minamiashigara, Kanagawa 250-0193 Japan
| |
Collapse
|
11
|
Fontaine BM, Martin KS, Garcia-Rodriguez JM, Jung C, Briggs L, Southwell JE, Jia X, Weinert EE. RNase I regulates Escherichia coli 2',3'-cyclic nucleotide monophosphate levels and biofilm formation. Biochem J 2018; 475:1491-1506. [PMID: 29555843 PMCID: PMC6452634 DOI: 10.1042/bcj20170906] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/13/2018] [Accepted: 03/16/2018] [Indexed: 12/15/2022]
Abstract
Regulation of nucleotide and nucleoside concentrations is critical for faithful DNA replication, transcription, and translation in all organisms, and has been linked to bacterial biofilm formation. Unusual 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) recently were quantified in mammalian systems, and previous reports have linked these nucleotides to cellular stress and damage in eukaryotes, suggesting an intriguing connection with nucleotide/nucleoside pools and/or cyclic nucleotide signaling. This work reports the first quantification of 2',3'-cNMPs in Escherichia coli and demonstrates that 2',3'-cNMP levels in E. coli are generated specifically from RNase I-catalyzed RNA degradation, presumably as part of a previously unidentified nucleotide salvage pathway. Furthermore, RNase I and 2',3'-cNMP levels are demonstrated to play an important role in controlling biofilm formation. This work identifies a physiological role for cytoplasmic RNase I and constitutes the first progress toward elucidating the biological functions of bacterial 2',3'-cNMPs.
Collapse
Affiliation(s)
- Benjamin M. Fontaine
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Kevin S. Martin
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | | | - Claire Jung
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Laura Briggs
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Jessica E. Southwell
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Xin Jia
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| | - Emily E. Weinert
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 USA
| |
Collapse
|
12
|
Eukaryotic-type serine/threonine kinase mediated phosphorylation at Thr 169 perturbs mycobacterial guanylate kinase activity. Biosci Rep 2017; 37:BSR20171048. [PMID: 28963370 PMCID: PMC5686395 DOI: 10.1042/bsr20171048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 09/23/2017] [Accepted: 09/25/2017] [Indexed: 01/22/2023] Open
Abstract
Guanylate kinase is an essential and conserved enzyme in nucleotide biosynthetic pathway that transfers phosphoryl group of ATP to GMP for yielding GDP. Here, we report the phosphorylation of guanylate kinase from Mycobacterium tuberculosis (mGmk) by eukaryotic-type Ser/Thr kinase, PknA. Mass spectrometric studies identified Thr101 and Thr169 as phosphorylatable residues in mGmk. To evaluate the significance of phosphorylation in these threonines, two point (T101A and T169A) and one double (T101A-T169A) mutants were generated. The kinase assay with these mutant proteins revealed the major contribution of Thr169 compared with Thr101 in the phosphorylation of mGmk. Kinetic analysis indicated that p-mGmk was deficient in its enzymatic activity compared with that of its un-phosphorylated counterpart. Surprisingly, its phosphoablated (T169A) as well as phosphomimic (T169E) variants exhibited decreased activity as was observed with p-mGmk. Structural analysis suggested that phosphorylation of Thr169 might affect its interaction with Arg166, which is crucial for the functioning of mGmk. In fact, the R166A and R166K mutant proteins displayed a drastic decrease in enzymatic activity compared with that of the wild-type mGmk. Molecular dynamics (MD) studies of mGmk revealed that upon phosphorylation of Thr169, the interactions of Arg165/Arg166 with Glu158, Asp121 and residues of the loop in GMP-binding domain are perturbed. Taken together, our results illuminate the mechanistic insights into phosphorylation-mediated modulation of the catalytic activity of mGmk.
Collapse
|
13
|
Zhou H, Liu Q, Shi T, Yu Y, Lu H. Genome-wide screen of fission yeast mutants for sensitivity to 6-azauracil, an inhibitor of transcriptional elongation. Yeast 2015; 32:643-55. [DOI: 10.1002/yea.3085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/23/2015] [Accepted: 06/26/2015] [Indexed: 01/10/2023] Open
Affiliation(s)
- Huan Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Qi Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Tianfang Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
- Shanghai Collaborative Innovation Centre for Biomanufacturing Technology; Shanghai 200237 People's Republic of China
| |
Collapse
|
14
|
Pérez-Torrado R, Llopis S, Perrone B, Gómez-Pastor R, Hube B, Querol A. Comparative genomic analysis reveals a critical role of de novo nucleotide biosynthesis for Saccharomyces cerevisiae virulence. PLoS One 2015; 10:e0122382. [PMID: 25816288 PMCID: PMC4376706 DOI: 10.1371/journal.pone.0122382] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/23/2015] [Indexed: 12/22/2022] Open
Abstract
In recent years, the number of human infection cases produced by the food related species Saccharomyces cerevisiae has increased. Whereas many strains of this species are considered safe, other 'opportunistic' strains show a high degree of potential virulence attributes and can cause infections in immunocompromised patients. Here we studied the genetic characteristics of selected opportunistic strains isolated from dietary supplements and also from patients by array comparative genomic hybridization. Our results show increased copy numbers of IMD genes in opportunistic strains, which are implicated in the de novo biosynthesis of the purine nucleotides pathway. The importance of this pathway for virulence of S. cerevisiae was confirmed by infections in immunodeficient murine models using a GUA1 mutant, a key gene of this pathway. We show that exogenous guanine, an end product of this pathway in its triphosphorylated form, increases the survival of yeast strains in ex vivo blood infections. Finally, we show the importance of the DNA damage response that activates dNTP biosynthesis in yeast cells during ex vivo blood infections. We conclude that opportunistic yeasts may use an enhanced de novo biosynthesis of the purine nucleotides pathway to increase survival and favor infections in the host.
Collapse
Affiliation(s)
| | - Silvia Llopis
- Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
| | - Benedetta Perrone
- Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
- Department of Agricultural, Forest and Food Sciences Microbiology and Food Technologies Unit University of Torino, Torino, Italy
| | - Rocío Gómez-Pastor
- Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute (HKI), Jena, Germany
- Friedrich Schiller University, Jena, Germany
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos, CSIC, Valencia, Spain
| |
Collapse
|
15
|
Ramos S, Chafsey I, Silva N, Hébraud M, Santos H, Capelo-Martinez JL, Poeta P, Igrejas G. Effect of vancomycin on the proteome of the multiresistant Enterococcus faecium SU18 strain. J Proteomics 2015; 113:378-87. [DOI: 10.1016/j.jprot.2014.10.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 10/03/2014] [Accepted: 10/20/2014] [Indexed: 11/25/2022]
|
16
|
Nosyreva VV, Mal’kina AG, Albanov AI, Trofimov BA. Modification of guanosine with cyanopropargylic alcohols. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
17
|
Akizu N, Cantagrel V, Schroth J, Cai N, Vaux K, McCloskey D, Naviaux RK, Van Vleet J, Fenstermaker AG, Silhavy JL, Scheliga JS, Toyama K, Morisaki H, Sonmez FM, Celep F, Oraby A, Zaki MS, Al-Baradie R, Faqeih EA, Saleh MAM, Spencer E, Rosti RO, Scott E, Nickerson E, Gabriel S, Morisaki T, Holmes EW, Gleeson JG. AMPD2 regulates GTP synthesis and is mutated in a potentially treatable neurodegenerative brainstem disorder. Cell 2013; 154:505-17. [PMID: 23911318 DOI: 10.1016/j.cell.2013.07.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 05/10/2013] [Accepted: 07/01/2013] [Indexed: 01/03/2023]
Abstract
Purine biosynthesis and metabolism, conserved in all living organisms, is essential for cellular energy homeostasis and nucleic acid synthesis. The de novo synthesis of purine precursors is under tight negative feedback regulation mediated by adenosine and guanine nucleotides. We describe a distinct early-onset neurodegenerative condition resulting from mutations in the adenosine monophosphate deaminase 2 gene (AMPD2). Patients have characteristic brain imaging features of pontocerebellar hypoplasia (PCH) due to loss of brainstem and cerebellar parenchyma. We found that AMPD2 plays an evolutionary conserved role in the maintenance of cellular guanine nucleotide pools by regulating the feedback inhibition of adenosine derivatives on de novo purine synthesis. AMPD2 deficiency results in defective GTP-dependent initiation of protein translation, which can be rescued by administration of purine precursors. These data suggest AMPD2-related PCH as a potentially treatable early-onset neurodegenerative disease.
Collapse
Affiliation(s)
- Naiara Akizu
- Neurogenetics Laboratory, Institute for Genomic Medicine, Rady Children's Hospital, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Kriel A, Bittner AN, Kim SH, Liu K, Tehranchi AK, Zou WY, Rendon S, Chen R, Tu BP, Wang JD. Direct regulation of GTP homeostasis by (p)ppGpp: a critical component of viability and stress resistance. Mol Cell 2012; 48:231-41. [PMID: 22981860 DOI: 10.1016/j.molcel.2012.08.009] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 07/12/2012] [Accepted: 08/02/2012] [Indexed: 10/27/2022]
Abstract
Cells constantly adjust their metabolism in response to environmental conditions, yet major mechanisms underlying survival remain poorly understood. We discover a posttranscriptional mechanism that integrates starvation response with GTP homeostasis to allow survival, enacted by the nucleotide (p)ppGpp, a key player in bacterial stress response and persistence. We reveal that (p)ppGpp activates global metabolic changes upon starvation, allowing survival by regulating GTP. Combining metabolomics with biochemical demonstrations, we find that (p)ppGpp directly inhibits the activities of multiple GTP biosynthesis enzymes. This inhibition results in robust and rapid GTP regulation in Bacillus subtilis, which we demonstrate is essential to maintaining GTP levels within a range that supports viability even in the absence of starvation. Correspondingly, without (p)ppGpp, gross GTP dysregulation occurs, revealing a vital housekeeping function of (p)ppGpp; in fact, loss of (p)ppGpp results in death from rising GTP, a severe and previously unknown consequence of GTP dysfunction.
Collapse
Affiliation(s)
- Allison Kriel
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Regulation of amino acid, nucleotide, and phosphate metabolism in Saccharomyces cerevisiae. Genetics 2012; 190:885-929. [PMID: 22419079 DOI: 10.1534/genetics.111.133306] [Citation(s) in RCA: 338] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Ever since the beginning of biochemical analysis, yeast has been a pioneering model for studying the regulation of eukaryotic metabolism. During the last three decades, the combination of powerful yeast genetics and genome-wide approaches has led to a more integrated view of metabolic regulation. Multiple layers of regulation, from suprapathway control to individual gene responses, have been discovered. Constitutive and dedicated systems that are critical in sensing of the intra- and extracellular environment have been identified, and there is a growing awareness of their involvement in the highly regulated intracellular compartmentalization of proteins and metabolites. This review focuses on recent developments in the field of amino acid, nucleotide, and phosphate metabolism and provides illustrative examples of how yeast cells combine a variety of mechanisms to achieve coordinated regulation of multiple metabolic pathways. Importantly, common schemes have emerged, which reveal mechanisms conserved among various pathways, such as those involved in metabolite sensing and transcriptional regulation by noncoding RNAs or by metabolic intermediates. Thanks to the remarkable sophistication offered by the yeast experimental system, a picture of the intimate connections between the metabolomic and the transcriptome is becoming clear.
Collapse
|
20
|
Martucci NM, Lamberti A, Vitagliano L, Cantiello P, Ruggiero I, Arcari P, Masullo M. The magic spot ppGpp influences in vitro the molecular and functional properties of the elongation factor 1α from the archaeon Sulfolobus solfataricus. Extremophiles 2012; 16:743-9. [PMID: 22772751 DOI: 10.1007/s00792-012-0470-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 06/21/2012] [Indexed: 12/01/2022]
Abstract
Guanosine tetra-phosphate (ppGpp), also known as "magic spot I", is a key molecule in the stringent control of most eubacteria and some eukarya. Here, we show that ppGpp affects the functional and molecular properties of the archaeal elongation factor 1α from Sulfolobus solfataricus (SsEF-1α). Indeed, ppGpp inhibited archaeal protein synthesis in vitro, even though the concentration required to get inhibition was higher than that required for the eubacterial and eukaryal systems. Regarding the partial reactions catalysed by SsEF-1α the effect produced by ppGpp on the affinity for aa-tRNA was lower than that measured in the presence of GTP but higher than that for GDP. Magic spot I was also able to bind SsEF-1α with an intermediate affinity in comparison to that displayed by GDP and GTP. Furthermore, ppGpp inhibited the intrinsic GTPase of SsEF-1α with a competitive behaviour. Finally, the binding of ppGpp to SsEF-1α rendered the elongation factor more resistant to heat treatment and the analysis of the molecular model of the complex between SsEF-1α and ppGpp suggests that this stabilisation arises from the charge optimisation on the surface of the protein.
Collapse
Affiliation(s)
- Nicola M Martucci
- Dipartimento di Studi delle Istituzioni e dei Sistemi Territoriali, Università degli Studi di Napoli Parthenope, Via Medina 40, 80133 Naples, Italy
| | | | | | | | | | | | | |
Collapse
|
21
|
Bergdahl B, Heer D, Sauer U, Hahn-Hägerdal B, van Niel EWJ. Dynamic metabolomics differentiates between carbon and energy starvation in recombinant Saccharomyces cerevisiae fermenting xylose. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:34. [PMID: 22587303 PMCID: PMC3462113 DOI: 10.1186/1754-6834-5-34] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 04/23/2012] [Indexed: 05/15/2023]
Abstract
BACKGROUND The concerted effects of changes in gene expression due to changes in the environment are ultimately reflected in the metabolome. Dynamics of metabolite concentrations under a certain condition can therefore give a description of the cellular state with a high degree of functional information. We used this potential to evaluate the metabolic status of two recombinant strains of Saccharomyces cerevisiae during anaerobic batch fermentation of a glucose/xylose mixture. Two isogenic strains were studied, differing only in the pathways used for xylose assimilation: the oxidoreductive pathway with xylose reductase (XR) and xylitol dehydrogenase (XDH) or the isomerization pathway with xylose isomerase (XI). The isogenic relationship between the two strains ascertains that the observed responses are a result of the particular xylose pathway and not due to unknown changes in regulatory systems. An increased understanding of the physiological state of these strains is important for further development of efficient pentose-utilizing strains for bioethanol production. RESULTS Using LC-MS/MS we determined the dynamics in the concentrations of intracellular metabolites in central carbon metabolism, nine amino acids, the purine nucleotides and redox cofactors. The general response to the transition from glucose to xylose was increased concentrations of amino acids and TCA-cycle intermediates, and decreased concentrations of sugar phosphates and redox cofactors. The two strains investigated had significantly different uptake rates of xylose which led to an enhanced response in the XI-strain. Despite the difference in xylose uptake rate, the adenylate energy charge remained high and stable around 0.8 in both strains. In contrast to the adenylate pool, large changes were observed in the guanylate pool. CONCLUSIONS The low uptake of xylose by the XI-strain led to several distinguished responses: depletion of key metabolites in glycolysis and NADPH, a reduced GTP/GDP ratio and accumulation of PEP and aromatic amino acids. These changes are strong indicators of carbon starvation. The XR/XDH-strain displayed few such traits. The coexistence of these traits and a stable adenylate charge indicates that xylose supplies energy to the cells but does not suppress a response similar to carbon starvation. Particular signals may play a role in the latter, of which the GTP/GMP ratio could be a candidate as it decreased significantly in both strains.
Collapse
Affiliation(s)
- Basti Bergdahl
- Applied Microbiology, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | | | - Uwe Sauer
- ETH Zurich, Zurich, 8093, Switzerland
| | | | - Ed WJ van Niel
- Applied Microbiology, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| |
Collapse
|