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Wang J, Cao Y, Shi D, Zhang Z, Li X, Chen C. Crucial Involvement of Heme Biosynthesis in Vegetative Growth, Development, Stress Response, and Fungicide Sensitivity of Fusarium graminearum. Int J Mol Sci 2024; 25:5268. [PMID: 38791308 PMCID: PMC11120706 DOI: 10.3390/ijms25105268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Heme biosynthesis is a highly conserved pathway from bacteria to higher animals. Heme, which serves as a prosthetic group for various enzymes involved in multiple biochemical processes, is essential in almost all species, making heme homeostasis vital for life. However, studies on the biological functions of heme in filamentous fungi are scarce. In this study, we investigated the role of heme in Fusarium graminearum. A mutant lacking the rate-limiting enzymes in heme synthesis, coproporphyrinogen III oxidase (Cpo) or ferrochelatase (Fc), was constructed using a homologous recombination strategy. The results showed that the absence of these enzymes was lethal to F. graminearum, but the growth defect could be rescued by the addition of hemin, so we carried out further studies with the help of hemin. The results demonstrated that heme was required for the activity of FgCyp51, and its absence increased the sensitivity to tebuconazole and led to the upregulation of FgCYP51 in F. graminearum. Additionally, heme plays an indispensable role in the life cycle of F. graminearum, which is essential for vegetative growth, conidiation, external stress response (especially oxidative stress), lipid accumulation, fatty acid β-oxidation, autophagy, and virulence.
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Affiliation(s)
| | | | | | | | | | - Changjun Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (J.W.); (Y.C.); (D.S.); (Z.Z.); (X.L.)
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2
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Duveau F, Cordier C, Chiron L, Le Bec M, Pouzet S, Séguin J, Llamosi A, Sorre B, Di Meglio JM, Hersen P. Yeast cell responses and survival during periodic osmotic stress are controlled by glucose availability. eLife 2024; 12:RP88750. [PMID: 38568203 PMCID: PMC10990491 DOI: 10.7554/elife.88750] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
Natural environments of living organisms are often dynamic and multifactorial, with multiple parameters fluctuating over time. To better understand how cells respond to dynamically interacting factors, we quantified the effects of dual fluctuations of osmotic stress and glucose deprivation on yeast cells using microfluidics and time-lapse microscopy. Strikingly, we observed that cell proliferation, survival, and signaling depend on the phasing of the two periodic stresses. Cells divided faster, survived longer, and showed decreased transcriptional response when fluctuations of hyperosmotic stress and glucose deprivation occurred in phase than when the two stresses occurred alternatively. Therefore, glucose availability regulates yeast responses to dynamic osmotic stress, showcasing the key role of metabolic fluctuations in cellular responses to dynamic stress. We also found that mutants with impaired osmotic stress response were better adapted to alternating stresses than wild-type cells, showing that genetic mechanisms of adaptation to a persistent stress factor can be detrimental under dynamically interacting conditions.
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Affiliation(s)
- Fabien Duveau
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d'Italie F-69364LyonFrance
| | - Céline Cordier
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Lionel Chiron
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Matthias Le Bec
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Sylvain Pouzet
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Julie Séguin
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
| | - Artémis Llamosi
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
| | - Benoit Sorre
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Jean-Marc Di Meglio
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
| | - Pascal Hersen
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
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3
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van Aalst ACA, van der Meulen IS, Jansen MLA, Mans R, Pronk JT. Co-cultivation of Saccharomyces cerevisiae strains combines advantages of different metabolic engineering strategies for improved ethanol yield. Metab Eng 2023; 80:151-162. [PMID: 37751790 DOI: 10.1016/j.ymben.2023.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023]
Abstract
Glycerol is the major organic byproduct of industrial ethanol production with the yeast Saccharomyces cerevisiae. Improved ethanol yields have been achieved with engineered S. cerevisiae strains in which heterologous pathways replace glycerol formation as the predominant mechanism for anaerobic re-oxidation of surplus NADH generated in biosynthetic reactions. Functional expression of heterologous phosphoribulokinase (PRK) and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) genes enables yeast cells to couple a net oxidation of NADH to the conversion of glucose to ethanol. In another strategy, NADH-dependent reduction of exogenous acetate to ethanol is enabled by introduction of a heterologous acetylating acetaldehyde dehydrogenase (A-ALD). This study explores potential advantages of co-cultivating engineered PRK-RuBisCO-based and A-ALD-based strains in anaerobic bioreactor batch cultures. Co-cultivation of these strains, which in monocultures showed reduced glycerol yields and improved ethanol yields, strongly reduced the formation of acetaldehyde and acetate, two byproducts that were formed in anaerobic monocultures of a PRK-RuBisCO-based strain. In addition, co-cultures on medium with low acetate-to-glucose ratios that mimicked those in industrial feedstocks completely removed acetate from the medium. Kinetics of co-cultivation processes and glycerol production could be optimized by tuning the relative inoculum sizes of the two strains. Co-cultivation of a PRK-RuBisCO strain with a Δgpd1 Δgpd2 A-ALD strain, which was unable to grow in the absence of acetate and evolved for faster anaerobic growth in acetate-supplemented batch cultures, further reduced glycerol formation but led to extended fermentation times. These results demonstrate the potential of using defined consortia of engineered S. cerevisiae strains for high-yield, minimal-waste ethanol production.
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Affiliation(s)
- Aafke C A van Aalst
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands
| | - Igor S van der Meulen
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands
| | - Mickel L A Jansen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613, AX, Delft, the Netherlands
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands.
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4
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Wang X, Li Y, Li X, Sun L, Feng Y, Sa F, Ge Y, Yang S, Liu Y, Li W, Cheng X. Transcriptome and metabolome profiling unveils the mechanisms of naphthalene acetic acid in promoting cordycepin synthesis in Cordyceps militaris. Front Nutr 2023; 10:1104446. [PMID: 36875834 PMCID: PMC9977999 DOI: 10.3389/fnut.2023.1104446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Cordycepin, an important active substance in Cordyceps militaris, possesses antiviral and other beneficial activities. In addition, it has been reported to effectively promote the comprehensive treatment of COVID-19 and thus has become a research hotspot. The addition of naphthalene acetic acid (NAA) is known to significantly improve the yield of cordycepin; however, its related molecular mechanism remains unclear. We conducted a preliminary study on C. militaris with different concentrations of NAA. We found that treatment with different concentrations of NAA inhibited the growth of C. militaris, and an increase in its concentration significantly improved the cordycepin content. In addition, we conducted a transcriptome and metabolomics association analysis on C. militaris treated with NAA to understand the relevant metabolic pathway of cordycepin synthesis under NAA treatment and elucidate the relevant regulatory network of cordycepin synthesis. Weighted gene co-expression network analysis (WGCNA), transcriptome, and metabolome association analysis revealed that genes and metabolites encoding cordycepin synthesis in the purine metabolic pathway varied significantly with the concentration of NAA. Finally, we proposed a metabolic pathway by analyzing the relationship between gene-gene and gene-metabolite regulatory networks, including the interaction of cordycepin synthesis key genes; key metabolites; purine metabolism; TCA cycle; pentose phosphate pathway; alanine, aspartate, and glutamate metabolism; and histidine metabolism. In addition, we found the ABC transporter pathway to be significantly enriched. The ABC transporters are known to transport numerous amino acids, such as L-glutamate, and participate in the amino acid metabolism that affects the synthesis of cordycepin. Altogether, multiple channels work together to double the cordycepin yield, thereby providing an important reference for the molecular network relationship between the transcription and metabolism of cordycepin synthesis.
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Affiliation(s)
- Xin Wang
- Shandong Key Laboratory of Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China
| | - Yin Li
- Yantai Hospital of Traditional Chinese Medicine, Yantai, China
| | - Xiue Li
- Shandong Key Laboratory of Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China
| | - Lei Sun
- College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Yetong Feng
- Shandong Key Laboratory of Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China
| | - Fangping Sa
- Shandong Key Laboratory of Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China
| | - Yupeng Ge
- Shandong Key Laboratory of Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China
| | - Shude Yang
- Shandong Key Laboratory of Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China
| | - Yu Liu
- Shandong Key Laboratory of Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China
| | - Weihuan Li
- Shandong Key Laboratory of Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China
| | - Xianhao Cheng
- Shandong Key Laboratory of Edible Mushroom Technology, School of Agriculture, Ludong University, Yantai, China
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Metabolic Mechanism and Physiological Role of Glycerol 3-Phosphate in Pseudomonas aeruginosa PAO1. mBio 2022; 13:e0262422. [PMID: 36218368 PMCID: PMC9765544 DOI: 10.1128/mbio.02624-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa is an important opportunistic pathogen that is lethal to cystic fibrosis (CF) patients. Glycerol generated during the degradation of phosphatidylcholine, the major lung surfactant in CF patients, could be utilized by P. aeruginosa. Previous studies have indicated that metabolism of glycerol by this bacterium contributes to its adaptation to and persistence in the CF lung environment. Here, we investigated the metabolic mechanisms of glycerol and its important metabolic intermediate glycerol 3-phosphate (G3P) in P. aeruginosa PAO1. We found that G3P homeostasis plays an important role in the growth and virulence factor production of P. aeruginosa PAO1. The G3P accumulation caused by the mutation of G3P dehydrogenase (GlpD) and exogenous glycerol led to impaired growth and reductions in pyocyanin synthesis, motilities, tolerance to oxidative stress, and resistance to kanamycin. Transcriptomic analysis indicates that the growth retardation caused by G3P stress is associated with reduced glycolysis and adenosine triphosphate (ATP) generation. Furthermore, two haloacid dehalogenase-like phosphatases (PA0562 and PA3172) that play roles in the dephosphorylation of G3P in strain PAO1 were identified, and their enzymatic properties were characterized. Our findings reveal the importance of G3P homeostasis and indicate that GlpD, the key enzyme for G3P catabolism, is a potential therapeutic target for the prevention and treatment of infections by this pathogen. IMPORTANCE In view of the intrinsic resistance of Pseudomonas aeruginosa to antibiotics and its potential to acquire resistance to current antibiotics, there is an urgent need to develop novel therapeutic options for the treatment of infections caused by this bacterium. Bacterial metabolic pathways have recently become a focus of interest as potential targets for the development of new antibiotics. In this study, we describe the mechanism of glycerol utilization in P. aeruginosa PAO1, which is an available carbon source in the lung environment. Our results reveal that the homeostasis of glycerol 3-phosphate (G3P), a pivotal intermediate in glycerol catabolism, is important for the growth and virulence factor production of P. aeruginosa PAO1. The mutation of G3P dehydrogenase (GlpD) and the addition of glycerol were found to reduce the tolerance of P. aeruginosa PAO1 to oxidative stress and to kanamycin. The findings highlight the importance of G3P homeostasis and suggest that GlpD is a potential drug target for the treatment of P. aeruginosa infections.
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6
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The regulatory mechanism of the yeast osmoresponse under different glucose concentrations. iScience 2022; 26:105809. [PMID: 36636353 PMCID: PMC9830198 DOI: 10.1016/j.isci.2022.105809] [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: 02/18/2022] [Revised: 07/20/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Cells constantly respond to environmental changes by modulating gene expression programs. These responses may demand substantial costs and, thus, affect cell growth. Understanding the regulation of these processes represents a key question in biology and biotechnology. Here, we studied the responses to osmotic stress in glucose-limited environments. By analyzing seventeen osmotic stress-induced genes and stress-activated protein kinase Hog1, we found that cells exhibited stronger osmotic gene expression response and larger integral of Hog1 nuclear localization during adaptation to osmotic stress under glucose-limited conditions than under glucose-rich conditions. We proposed and verified that in glucose-limited environment, glycolysis intermediates (representing "reserve flux") were limited, which required cells to express more glycerol-production enzymes for stress adaptation. Consequently, the regulatory mechanism of osmoresponse was derived in the presence and absence of such reserve flux. Further experiments suggested that this reserve flux-dependent stress-defense strategy may be a general principle under nutrient-limited environments.
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7
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Top-Down, Knowledge-Based Genetic Reduction of Yeast Central Carbon Metabolism. mBio 2022; 13:e0297021. [PMID: 36129294 PMCID: PMC9600970 DOI: 10.1128/mbio.02970-21] [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] [Indexed: 11/20/2022] Open
Abstract
Saccharomyces cerevisiae, whose evolutionary past includes a whole-genome duplication event, is characterized by a mosaic genome configuration with substantial apparent genetic redundancy. This apparent redundancy raises questions about the evolutionary driving force for genomic fixation of “minor” paralogs and complicates modular and combinatorial metabolic engineering strategies. While isoenzymes might be important in specific environments, they could be dispensable in controlled laboratory or industrial contexts. The present study explores the extent to which the genetic complexity of the central carbon metabolism (CCM) in S. cerevisiae, here defined as the combination of glycolysis, the pentose phosphate pathway, the tricarboxylic acid cycle, and a limited number of related pathways and reactions, can be reduced by elimination of (iso)enzymes without major negative impacts on strain physiology. Cas9-mediated, groupwise deletion of 35 of the 111 genes yielded a “minimal CCM” strain which, despite the elimination of 32% of CCM-related proteins, showed only a minimal change in phenotype on glucose-containing synthetic medium in controlled bioreactor cultures relative to a congenic reference strain. Analysis under a wide range of other growth and stress conditions revealed remarkably few phenotypic changes from the reduction of genetic complexity. Still, a well-documented context-dependent role of GPD1 in osmotolerance was confirmed. The minimal CCM strain provides a model system for further research into genetic redundancy of yeast genes and a platform for strategies aimed at large-scale, combinatorial remodeling of yeast CCM.
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8
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Blomberg A. Yeast osmoregulation - glycerol still in pole position. FEMS Yeast Res 2022; 22:6655991. [PMID: 35927716 PMCID: PMC9428294 DOI: 10.1093/femsyr/foac035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/29/2022] [Accepted: 08/02/2022] [Indexed: 11/14/2022] Open
Abstract
In response to osmotic dehydration cells sense, signal, alter gene expression, and metabolically counterbalance osmotic differences. The main compatible solute/osmolyte that accumulates in yeast cells is glycerol, which is produced from the glycolytic intermediate dihydroxyacetone phosphate. This review covers recent advancements in understanding mechanisms involved in sensing, signaling, cell-cycle delays, transcriptional responses as well as post-translational modifications on key proteins in osmoregulation. The protein kinase Hog1 is a key-player in many of these events, however, there is also a growing body of evidence for important Hog1-independent mechanisms playing vital roles. Several missing links in our understanding of osmoregulation will be discussed and future avenues for research proposed. The review highlights that this rather simple experimental system—salt/sorbitol and yeast—has developed into an enormously potent model system unravelling important fundamental aspects in biology.
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Affiliation(s)
- Anders Blomberg
- Dept. of Chemistry and Molecular Biology, University of Gothenburg, Sweden
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9
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van Aalst AC, de Valk SC, van Gulik WM, Jansen ML, Pronk JT, Mans R. Pathway engineering strategies for improved product yield in yeast-based industrial ethanol production. Synth Syst Biotechnol 2022; 7:554-566. [PMID: 35128088 PMCID: PMC8792080 DOI: 10.1016/j.synbio.2021.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/16/2022] Open
Abstract
Product yield on carbohydrate feedstocks is a key performance indicator for industrial ethanol production with the yeast Saccharomyces cerevisiae. This paper reviews pathway engineering strategies for improving ethanol yield on glucose and/or sucrose in anaerobic cultures of this yeast by altering the ratio of ethanol production, yeast growth and glycerol formation. Particular attention is paid to strategies aimed at altering energy coupling of alcoholic fermentation and to strategies for altering redox-cofactor coupling in carbon and nitrogen metabolism that aim to reduce or eliminate the role of glycerol formation in anaerobic redox metabolism. In addition to providing an overview of scientific advances we discuss context dependency, theoretical impact and potential for industrial application of different proposed and developed strategies.
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Affiliation(s)
- Aafke C.A. van Aalst
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Sophie C. de Valk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Walter M. van Gulik
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Mickel L.A. Jansen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613, AX Delft, the Netherlands
| | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ Delft, the Netherlands
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Lv G, Zhu Y, Cheng X, Cao Y, Zeng B, Liu X, He B. Transcriptomic Responses of Cordyceps militaris to Salt Treatment During Cordycepins Production. Front Nutr 2022; 8:793795. [PMID: 35004818 PMCID: PMC8733472 DOI: 10.3389/fnut.2021.793795] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Cordycepin is a major bioactive compound found in Cordyceps militaris (C. militaris) that exhibits a broad spectrum of biological activities. Hence, it is potentially a bioactive ingredient of pharmaceutical and cosmetic products. However, overexploitation and low productivity of natural C. militaris is a barrier to commercialization, which leads to insufficient supply to meet its existing market demands. In this study, a preliminary study of distinct concentrations of salt treatments toward C. militaris was conducted. Although the growth of C. militaris was inhibited by different salt treatments, the cordycepin production increased significantly accompanied by the increment of salt concentration. Among them, the content of cordycepin in the 7% salt-treated group was five-fold higher than that of the control group. Further transcriptome analysis of samples with four salt concentrations, coupled with Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, several differentially expressed genes (DEGs) were found. Finally, dynamic changes of the expression patterns of four genes involved in the cordycepin biosynthesis pathway were observed by the quantitative real-time PCR. Taken together, our study provides a global transcriptome characterization of the salt treatment adaptation process in C. militaris and facilitates the construction of industrial strains with a high cordycepin production and salt tolerance.
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Affiliation(s)
- Gongbo Lv
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-innovation Center for in-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yue Zhu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-innovation Center for in-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Xiaojie Cheng
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yan Cao
- Information Institute of Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Bin Zeng
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-innovation Center for in-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China.,College of Pharmacy, Shenzhen Technology University, Shenzhen, China
| | - Xinping Liu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-innovation Center for in-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Bin He
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-innovation Center for in-vitro Diagnostic Reagents and Devices of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, China
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11
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Dekker WJC, Jürgens H, Ortiz-Merino RA, Mooiman C, van den Berg R, Kaljouw A, Mans R, Pronk JT. OUP accepted manuscript. FEMS Yeast Res 2022; 22:6523363. [PMID: 35137036 PMCID: PMC8862043 DOI: 10.1093/femsyr/foac007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/26/2022] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
While thermotolerance is an attractive trait for yeasts used in industrial ethanol production, oxygen requirements of known thermotolerant species are incompatible with process requirements. Analysis of oxygen-sufficient and oxygen-limited chemostat cultures of the facultatively fermentative, thermotolerant species Ogataea parapolymorpha showed its minimum oxygen requirements to be an order of magnitude larger than those reported for the thermotolerant yeast Kluyveromyces marxianus. High oxygen requirements of O. parapolymorpha coincided with a near absence of glycerol, a key NADH/NAD+ redox-cofactor-balancing product in many other yeasts, in oxygen-limited cultures. Genome analysis indicated absence of orthologs of the Saccharomyces cerevisiae glycerol-3-phosphate-phosphatase genes GPP1 and GPP2. Co-feeding of acetoin, whose conversion to 2,3-butanediol enables reoxidation of cytosolic NADH, supported a 2.5-fold increase of the biomass concentration in oxygen-limited cultures. An O. parapolymorpha strain in which key genes involved in mitochondrial reoxidation of NADH were inactivated did produce glycerol, but transcriptome analysis did not reveal a clear candidate for a responsible phosphatase. Expression of S. cerevisiae GPD2, which encodes NAD+-dependent glycerol-3-phosphate dehydrogenase, and GPP1 supported increased glycerol production by oxygen-limited chemostat cultures of O. parapolymorpha. These results identify dependence on respiration for NADH reoxidation as a key contributor to unexpectedly high oxygen requirements of O. parapolymorpha.
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Affiliation(s)
- Wijbrand J C Dekker
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Hannes Jürgens
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Christiaan Mooiman
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Remon van den Berg
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Astrid Kaljouw
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jack T Pronk
- Corresponding author: Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands. Tel: +31 15 2783214; E-mail:
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12
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Mavrommati M, Daskalaki A, Papanikolaou S, Aggelis G. Adaptive laboratory evolution principles and applications in industrial biotechnology. Biotechnol Adv 2021; 54:107795. [PMID: 34246744 DOI: 10.1016/j.biotechadv.2021.107795] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/11/2021] [Accepted: 07/05/2021] [Indexed: 12/20/2022]
Abstract
Adaptive laboratory evolution (ALE) is an innovative approach for the generation of evolved microbial strains with desired characteristics, by implementing the rules of natural selection as presented in the Darwinian Theory, on the laboratory bench. New as it might be, it has already been used by several researchers for the amelioration of a variety of characteristics of widely used microorganisms in biotechnology. ALE is used as a tool for the deeper understanding of the genetic and/or metabolic pathways of evolution. Another important field targeted by ALE is the manufacturing of products of (high) added value, such as ethanol, butanol and lipids. In the current review, we discuss the basic principles and techniques of ALE, and then we focus on studies where it has been applied to bacteria, fungi and microalgae, aiming to improve their performance to biotechnological procedures and/or inspect the genetic background of evolution. We conclude that ALE is a promising and efficacious method that has already led to the acquisition of useful new microbiological strains in biotechnology and could possibly offer even more interesting results in the future.
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Affiliation(s)
- Maria Mavrommati
- Unit of Microbiology, Department of Biology, Division of Genetics, Cell Biology and Development, University of Patras, 26504 Patras, Greece; Laboratory of Food Microbiology and Biotechnology, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece
| | - Alexandra Daskalaki
- Unit of Microbiology, Department of Biology, Division of Genetics, Cell Biology and Development, University of Patras, 26504 Patras, Greece
| | - Seraphim Papanikolaou
- Laboratory of Food Microbiology and Biotechnology, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece
| | - George Aggelis
- Unit of Microbiology, Department of Biology, Division of Genetics, Cell Biology and Development, University of Patras, 26504 Patras, Greece.
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13
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Schikora-Tamarit MÀ, Marcet-Houben M, Nosek J, Gabaldón T. Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi. Open Biol 2021; 11:200362. [PMID: 33906412 PMCID: PMC8080010 DOI: 10.1098/rsob.200362] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Oxidative phosphorylation is among the most conserved mitochondrial pathways. However, one of the cornerstones of this pathway, the multi-protein complex NADH : ubiquinone oxidoreductase (complex I) has been lost multiple independent times in diverse eukaryotic lineages. The causes and consequences of these convergent losses remain poorly understood. Here, we used a comparative genomics approach to reconstruct evolutionary paths leading to complex I loss and infer possible evolutionary scenarios. By mining available mitochondrial and nuclear genomes, we identified eight independent events of mitochondrial complex I loss across eukaryotes, of which six occurred in fungal lineages. We focused on three recent loss events that affect closely related fungal species, and inferred genomic changes convergently associated with complex I loss. Based on these results, we predict novel complex I functional partners and relate the loss of complex I with the presence of increased mitochondrial antioxidants, higher fermentative capabilities, duplications of alternative dehydrogenases, loss of alternative oxidases and adaptation to antifungal compounds. To explain these findings, we hypothesize that a combination of previously acquired compensatory mechanisms and exposure to environmental triggers of oxidative stress (such as hypoxia and/or toxic chemicals) induced complex I loss in fungi.
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Affiliation(s)
- Miquel Àngel Schikora-Tamarit
- Life Sciences Department, Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona, 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Marina Marcet-Houben
- Life Sciences Department, Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona, 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Toni Gabaldón
- Life Sciences Department, Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona, 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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14
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Hernández-Fernández J, Pinzón-Velasco A, López EA, Rodríguez-Becerra P, Mariño-Ramírez L. Transcriptional Analyses of Acute Exposure to Methylmercury on Erythrocytes of Loggerhead Sea Turtle. TOXICS 2021; 9:70. [PMID: 33805397 PMCID: PMC8066450 DOI: 10.3390/toxics9040070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 01/09/2023]
Abstract
To understand changes in enzyme activity and gene expression as biomarkers of exposure to methylmercury, we exposed loggerhead turtle erythrocytes (RBCs) to concentrations of 0, 1, and 5 mg L-1 of MeHg and de novo transcriptome were assembled using RNA-seq. The analysis of differentially expressed genes (DEGs) indicated that 79 unique genes were dysregulated (39 upregulated and 44 downregulated genes). The results showed that MeHg altered gene expression patterns as a response to the cellular stress produced, reflected in cell cycle regulation, lysosomal activity, autophagy, calcium regulation, mitochondrial regulation, apoptosis, and regulation of transcription and translation. The analysis of DEGs showed a low response of the antioxidant machinery to MeHg, evidenced by the fact that genes of early response to oxidative stress were not dysregulated. The RBCs maintained a constitutive expression of proteins that represented a good part of the defense against reactive oxygen species (ROS) induced by MeHg.
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Affiliation(s)
- Javier Hernández-Fernández
- Department of Natural and Environmental Science, Marine Biology Program, Faculty of Science and Engineering, Genetics, Molecular Biology and Bioinformatic Research Group–GENBIMOL, Jorge Tadeo Lozano University, Cra. 4 No 22-61, Bogotá 110311, Colombia;
- Faculty of Sciences, Department of Biology, Pontificia Universidad Javeriana, Calle 45, Cra. 7, Bogotá 110231, Colombia
| | - Andrés Pinzón-Velasco
- Bioinformática y Biología de Sistemas, Universidad Nacional de Colombia, Calle 45, Cra. 30, Bogotá 111321, Colombia;
| | - Ellie Anne López
- IDEASA Research Group-Environment and Sustainability, Institute of Environmental Studies and Services, Sergio Arboleda University, Bogotá 111711, Colombia;
| | - Pilar Rodríguez-Becerra
- Department of Natural and Environmental Science, Marine Biology Program, Faculty of Science and Engineering, Genetics, Molecular Biology and Bioinformatic Research Group–GENBIMOL, Jorge Tadeo Lozano University, Cra. 4 No 22-61, Bogotá 110311, Colombia;
| | - Leonardo Mariño-Ramírez
- NCBI, NLM, NIH Computational Biology Branch, Building 38A, Room 6S614M 8600 Rockville Pike, MSC 6075, Bethesda, MD 20894-6075, USA;
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15
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Possik E, Al-Mass A, Peyot ML, Ahmad R, Al-Mulla F, Madiraju SRM, Prentki M. New Mammalian Glycerol-3-Phosphate Phosphatase: Role in β-Cell, Liver and Adipocyte Metabolism. Front Endocrinol (Lausanne) 2021; 12:706607. [PMID: 34326816 PMCID: PMC8313997 DOI: 10.3389/fendo.2021.706607] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/25/2021] [Indexed: 11/25/2022] Open
Abstract
Cardiometabolic diseases, including type 2 diabetes, obesity and non-alcoholic fatty liver disease, have enormous impact on modern societies worldwide. Excess nutritional burden and nutri-stress together with sedentary lifestyles lead to these diseases. Deranged glucose, fat, and energy metabolism is at the center of nutri-stress, and glycolysis-derived glycerol-3-phosphate (Gro3P) is at the crossroads of these metabolic pathways. Cellular levels of Gro3P can be controlled by its synthesis, utilization or hydrolysis. The belief that mammalian cells do not possess an enzyme that hydrolyzes Gro3P, as in lower organisms and plants, is challenged by our recent work showing the presence of a Gro3P phosphatase (G3PP) in mammalian cells. A previously described phosphoglycolate phosphatase (PGP) in mammalian cells, with no established physiological function, has been shown to actually function as G3PP, under physiological conditions, particularly at elevated glucose levels. In the present review, we summarize evidence that supports the view that G3PP plays an important role in the regulation of gluconeogenesis and fat storage in hepatocytes, glucose stimulated insulin secretion and nutri-stress in β-cells, and lipogenesis in adipocytes. We provide a balanced perspective on the pathophysiological significance of G3PP in mammals with specific reference to cardiometabolic diseases.
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Affiliation(s)
- Elite Possik
- Departments of Nutrition, Biochemistry and Molecular Medicine, and Montreal Diabetes Research Center, CRCHUM, Montréal, QC, Canada
| | - Anfal Al-Mass
- Departments of Nutrition, Biochemistry and Molecular Medicine, and Montreal Diabetes Research Center, CRCHUM, Montréal, QC, Canada
- Department of Medicine, McGill University, Montréal, QC, Canada
| | - Marie-Line Peyot
- Departments of Nutrition, Biochemistry and Molecular Medicine, and Montreal Diabetes Research Center, CRCHUM, Montréal, QC, Canada
| | - Rasheed Ahmad
- Immunology & Microbiology Department, Dasman Diabetes Institute, Dasman, Kuwait
| | - Fahd Al-Mulla
- Immunology & Microbiology Department, Dasman Diabetes Institute, Dasman, Kuwait
| | - S. R. Murthy Madiraju
- Departments of Nutrition, Biochemistry and Molecular Medicine, and Montreal Diabetes Research Center, CRCHUM, Montréal, QC, Canada
- *Correspondence: Marc Prentki, ; S. R. Murthy Madiraju,
| | - Marc Prentki
- Departments of Nutrition, Biochemistry and Molecular Medicine, and Montreal Diabetes Research Center, CRCHUM, Montréal, QC, Canada
- *Correspondence: Marc Prentki, ; S. R. Murthy Madiraju,
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16
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Kryachko Y, Batbayar B, Tanaka T, Nickerson MT, Korber DR. Production of glycerol by Lactobacillus plantarum NRRL B-4496 and formation of hexamine during fermentation of pea protein enriched flour. J Biotechnol 2020; 323:331-340. [PMID: 32950562 DOI: 10.1016/j.jbiotec.2020.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/20/2022]
Abstract
Suspensions of pea protein enriched flour (PP) inoculated with Lactobacillus plantarum NRRL B-4496 and uninoculated PP suspensions were incubated in vials covered with airtight caps. Organic compound compositions of fermented and unfermented PP suspensions (F-PP and U-PP, respectively) were analyzed using solid phase microextraction (SPME) coupled with gas chromatography - mass-spectrometry (GCMS). Acetic acid was detected in all samples; pH dropped from pH 6.5 to pH 4.1 in L. plantarum F-PP and to pH 5.3 in uninoculated F-PP. Abundance of acetic acid and minuscule presence of lactic acid in L. plantarum F-PP suggested that fermentation proceeded preferentially via the pyruvate formate lyase (PFL) pathway. Nonetheless, glycerol appeared to be the most abundant compound in L. plantarum F-PP samples; colorimetric analysis indicated that its average concentration in these samples was 1.05 g/L. A metabolic switch from the PFL pathway to glycerol production might occur due to acidity tolerance limitations of L. plantarum, glycerol production being associated with the release of phosphate, which can act as a buffer. Fermentation of PP by L. plantarum also led to formation of hexamine, which is a known food preservation agent. Presence of naturally formed hexamine and glycerol in food products may render using chemical additives needless.
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Affiliation(s)
- Yuriy Kryachko
- Department of Food and Bioproduct Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Barkhas Batbayar
- Department of Food and Bioproduct Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Takuji Tanaka
- Department of Food and Bioproduct Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Michael T Nickerson
- Department of Food and Bioproduct Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Darren R Korber
- Department of Food and Bioproduct Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada.
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17
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Li J, Paulo JA, Nusinow DP, Huttlin EL, Gygi SP. Investigation of Proteomic and Phosphoproteomic Responses to Signaling Network Perturbations Reveals Functional Pathway Organizations in Yeast. Cell Rep 2020; 29:2092-2104.e4. [PMID: 31722220 PMCID: PMC7382779 DOI: 10.1016/j.celrep.2019.10.034] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/30/2019] [Accepted: 10/09/2019] [Indexed: 12/25/2022] Open
Abstract
Governance of protein phosphorylation by kinases and phosphatases constitutes an essential regulatory network in eukaryotic cells. Network dysregulation leads to severe consequences and is often a key factor in disease pathogenesis. Previous studies revealed multiple roles for protein phosphorylation and pathway structures in cellular functions from different perspectives. We seek to understand the roles of kinases and phosphatases from a protein homeostasis point of view. Using a streamlined tandem mass tag (SL-TMT) strategy, we systematically measure proteomic and phosphoproteomic responses to perturbations of phosphorylation signaling networks in yeast deletion strains. Our results emphasize the requirement for protein normalization for more complete interpretation of phosphorylation data. Functional relationships between kinases and phosphatases were characterized at both proteome and phosphoproteome levels in three ways: (1) Gene Ontology enrichment analysis, (2) Δgene-Δgene correlation networks, and (3) molecule covariance networks. This resource illuminates kinase and phosphatase functions and pathway organizations.
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Affiliation(s)
- Jiaming Li
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - David P Nusinow
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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18
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Ferreira C, Couceiro J, Família C, Jardim C, Antas P, Santos CN, Outeiro TF, Tenreiro S, Quintas A. The synthetic cannabinoid JWH-018 modulates Saccharomyces cerevisiae energetic metabolism. FEMS Yeast Res 2020; 19:5521208. [PMID: 31329229 DOI: 10.1093/femsyr/foz042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023] Open
Abstract
Synthetic cannabinoids are a group of novel psychoactive substances with similar properties to Δ9-THC. Among the vast number of synthetic cannabinoids, designed to be tested in clinical trials, JWH-018 was the first novel psychoactive substance found in the recreational drug marketplace. The consumption of JWH-018 shows typical effects of CB1 agonists including sedation, cognitive dysfunction, tachycardia, postural hypotension, dry mouth, ataxia and psychotropic effects, but appeared to be more potent than Δ9-THC. However, studies on human cells have shown that JWH-018 toxicity depends on the cellular line used. Despite these studies, the underlying molecular mechanisms to JWH-018 action has not been clarified yet. To understand the impact of JWH-018 at molecular and cellular level, we used Saccharomyces cerevisiae as a model. The results showed an increase in yeast growth rate in the presence of this synthetic cannabinoid due to an enhancement in the glycolytic flux at expense of a decrease in pentose phosphate pathway, judging by 2D-Gel proteomic analysis, qRT-PCR experiments and ATP measurements. Overall, our results provide insights into molecular mechanisms of JWH-018 action, also indicating that Saccharomyces cerevisiae is a good model to study synthetic cannabinoids.
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Affiliation(s)
- Carla Ferreira
- Molecular Pathology and Forensic Biochemistry Laboratory, Centro de Investigação Interdisciplinar Egas Moniz, P-2825-084 Caparica, Portugal.,Laboratório de Ciências Forenses e Psicológicas Egas Moniz, Campus Universitário - Quinta da Granja, Monte de Caparica, P-2825-084 Caparica, Portugal.,Faculty of Medicine of Porto University, Al. Prof. Hernâni Monteiro, P-4200-319 Porto, Portugal
| | - Joana Couceiro
- Molecular Pathology and Forensic Biochemistry Laboratory, Centro de Investigação Interdisciplinar Egas Moniz, P-2825-084 Caparica, Portugal.,Laboratório de Ciências Forenses e Psicológicas Egas Moniz, Campus Universitário - Quinta da Granja, Monte de Caparica, P-2825-084 Caparica, Portugal
| | - Carlos Família
- Molecular Pathology and Forensic Biochemistry Laboratory, Centro de Investigação Interdisciplinar Egas Moniz, P-2825-084 Caparica, Portugal.,Laboratório de Ciências Forenses e Psicológicas Egas Moniz, Campus Universitário - Quinta da Granja, Monte de Caparica, P-2825-084 Caparica, Portugal
| | - Carolina Jardim
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, P-2780-901 Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, P-2780-157 Oeiras, Portugal
| | - Pedro Antas
- CEDOC - Chronic Diseases Research Center, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, P-1150-082 Lisboa, Portugal
| | - Cláudia N Santos
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, P-2780-901 Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, P-2780-157 Oeiras, Portugal.,CEDOC - Chronic Diseases Research Center, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, P-1150-082 Lisboa, Portugal
| | - Tiago F Outeiro
- CEDOC - Chronic Diseases Research Center, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, P-1150-082 Lisboa, Portugal.,Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Waldweg 33. Göttingen P37073, Germany.,Institute of Neuroscience, Medical School, Newcastle University, Framlington Place, Newcastle Upon Tyne P-NE1 7RU, UK.,Max Planck Institute for Experimental Medicine, Hermann Rein Street 3. P-37075 Göttingen, Germany
| | - Sandra Tenreiro
- CEDOC - Chronic Diseases Research Center, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, P-1150-082 Lisboa, Portugal
| | - Alexandre Quintas
- Molecular Pathology and Forensic Biochemistry Laboratory, Centro de Investigação Interdisciplinar Egas Moniz, P-2825-084 Caparica, Portugal.,Laboratório de Ciências Forenses e Psicológicas Egas Moniz, Campus Universitário - Quinta da Granja, Monte de Caparica, P-2825-084 Caparica, Portugal
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19
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Martho KF, Brustolini OJB, Vasconcelos AT, Vallim MA, Pascon RC. The Glycerol Phosphatase Gpp2: A Link to Osmotic Stress, Sulfur Assimilation and Virulence in Cryptococcus neoformans. Front Microbiol 2019; 10:2728. [PMID: 31849880 PMCID: PMC6901960 DOI: 10.3389/fmicb.2019.02728] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/08/2019] [Indexed: 12/13/2022] Open
Abstract
Cryptococcus neoformans is an opportunist fungal pathogen that causes meningoencephalitis in immunocompromised patients. During infection, this basidiomycete yeast has to adapt to several adverse conditions, especially nutrient availability. The interruption on various amino acid biosynthetic pathways and on amino acid uptake causes reduced viability, inability to cope with various stresses, failure in virulence factors expression and avirulence in animal model of infection. The sulfur amino acid biosynthesis and uptake is an important feature for pathogen survival in vivo and in vitro. Our previous work demonstrates that C. neoformans Cys3 BZip transcription factor controls the gene expression in several steps of the sulfur assimilation and sulfur amino acid biosynthesis. Also, we have shown that Gpp2 phosphatase modulates Cys3 activity. In Saccharomyces cerevisiae Gpp2 is induced in response to hyper osmotic or oxidative stress and during diauxic shift. In this work, we will show that, in C. neoformans, Gpp2 is required to respond to stresses, mainly osmotic stress; also its transcription is induced during exposure to NaCl. Global transcriptional profile of gpp2Δ by RNAseq shows that CYS3 and other genes in the sulfur assimilation pathway are up regulated, which is consistent with our previous report, in which Gpp2 acts by avoiding Cys3 accumulation and nuclear localization. In addition, several transporters genes, especially amino acid permeases and oxidative stress genes are induced in the gpp2Δ strain; on the contrary, genes involved in glucose and tricarboxylic acid metabolism are down regulated. gpp2Δ strain fails to express virulence factors, as melanin, phospholipase, urease and has virulence attenuation in Galleria mellonella. Our data suggest that Gpp2 is an important factor for general pathogen adaptation to various stresses and also to the host, and perhaps it could be an interesting target for therapeutic use.
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Affiliation(s)
- Kevin Felipe Martho
- Department of Biological Sciences, Campus Diadema, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Otávio J B Brustolini
- Laboratório Nacional de Computação Científica - LNCC, Labinfo - Laboratório de Bioinformática, Petrópolis, Brazil
| | - Ana Tereza Vasconcelos
- Laboratório Nacional de Computação Científica - LNCC, Labinfo - Laboratório de Bioinformática, Petrópolis, Brazil
| | - Marcelo A Vallim
- Department of Biological Sciences, Campus Diadema, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Renata C Pascon
- Department of Biological Sciences, Campus Diadema, Universidade Federal de São Paulo, São Paulo, Brazil
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20
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Joshua IM, Höfken T. Ste20 and Cla4 modulate the expression of the glycerol biosynthesis enzyme Gpd1 by a novel MAPK-independent pathway. Biochem Biophys Res Commun 2019; 517:611-616. [PMID: 31395335 DOI: 10.1016/j.bbrc.2019.07.072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 07/19/2019] [Indexed: 11/29/2022]
Abstract
p21-activated kinases (PAKs) are important signalling molecules with a wide range of functions. In budding yeast, the main PAKs Ste20 and Cla4 regulate the response to hyperosmotic stress, which is an excellent model for the adaptation to changing environmental conditions. In this pathway, the only known function of Ste20 and Cla4 is the activation of a mitogen-activated protein kinase (MAPK) cascade through Ste11. This eventually leads to increased transcription of glycerol biosynthesis genes, the most important response to hyperosmotic shock. Here, we show that Ste20 and Cla4 not only stimulate transcription, they also bind to the glycerol biosynthesis enzymes Gpd1, Gpp1 and Gpp2. Protein levels of Gpd1, the enzyme that catalyzes the rate limiting step in glycerol synthesis, positively correlate with glucose availability. Using a chemical genetics approach, we find that simultaneous inactivation of STE20 and CLA4 reduces the glucose-induced increase of Gpd1 levels, whereas the deletion of either STE20 or CLA4 alone has no effect. This is also observed for the hyperosmotic stress-induced increase of Gpd1 levels. Importantly, under both conditions the deletion of STE11 has no effect on Gpd1 induction. These observations suggest that Ste20 and Cla4 not only have a role in the transcriptional regulation of GPD1 through Ste11. They also seem to modulate GPD1 expression at another level such as translation or protein degradation.
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Affiliation(s)
| | - Thomas Höfken
- Division of Biosciences, Brunel University London, UK.
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21
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Tumukunde E, Li D, Qin L, Li Y, Shen J, Wang S, Yuan J. Osmotic-Adaptation Response of sakA/hogA Gene to Aflatoxin Biosynthesis, Morphology Development and Pathogenicity in Aspergillus flavus. Toxins (Basel) 2019; 11:toxins11010041. [PMID: 30646608 PMCID: PMC6356625 DOI: 10.3390/toxins11010041] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/19/2018] [Accepted: 01/11/2019] [Indexed: 02/06/2023] Open
Abstract
Aspergillus flavus is one of the fungi from the big family of Aspergillus genus and it is capable of colonizing a large number of seed/crops and living organisms such as animals and human beings. SakA (also called hogA/hog1) is an integral part of the mitogen activated protein kinase signal of the high osmolarity glycerol pathway. In this study, the AfsakA gene was deleted (∆AfsakA) then complemented (∆AfsakA::AfsakA) using homologous recombination and the osmotic stress was induced by 1.2 mol/L D-sorbital and 1.2 mol/L sodium chloride. The result showed that ∆AfsakA mutant caused a significant influence on conidial formation compared to wild-type and ∆AfsakA::AfsakA strains. It was also found that AfsakA responds to both the osmotic stress and the cell wall stress. In the absence of osmotic stress, ∆AfsakA mutant produced more sclerotia in contrast to other strains, whereas all strains failed to generate sclerotia under osmotic stress. Furthermore, the deletion of AfsakA resulted in the increase of Aflatoxin B1 production compared to other strains. The virulence assay on both maize kernel and peanut seeds showed that ∆AfsakA strain drastically produced more conidia and Aflatoxin B1 than wild-type and complementary strains. AfSakA-mCherry was located to the cytoplasm in the absence of osmotic stress, while it translocated to the nucleus upon exposure to the osmotic stimuli. This study provides new insights on the development and evaluation of aflatoxin biosynthesis and also provides better understanding on how to prevent Aspergillus infections which would be considered the first step towards the prevention of the seeds damages caused by A. flavus.
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Affiliation(s)
- Elisabeth Tumukunde
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of the Ministry of Education and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Ding Li
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of the Ministry of Education and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Ling Qin
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of the Ministry of Education and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yu Li
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of the Ministry of Education and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Jiaojiao Shen
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of the Ministry of Education and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Shihua Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of the Ministry of Education and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Jun Yuan
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of the Ministry of Education and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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22
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Effect of Trehalose and Glycerol on the Resistance of Recombinant Saccharomyces cerevisiae Strains to Desiccation, Freeze-Thaw and Osmotic Stresses. SCIENCE AND INNOVATION 2018. [DOI: 10.15407/scine14.06.073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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23
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Xu YF, Lu W, Chen JC, Johnson SA, Gibney PA, Thomas DG, Brown G, May AL, Campagna SR, Yakunin AF, Botstein D, Rabinowitz JD. Discovery and Functional Characterization of a Yeast Sugar Alcohol Phosphatase. ACS Chem Biol 2018; 13:3011-3020. [PMID: 30240188 DOI: 10.1021/acschembio.8b00804] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Sugar alcohols (polyols) exist widely in nature. While some specific sugar alcohol phosphatases are known, there is no known phosphatase for some important sugar alcohols (e.g., sorbitol-6-phosphate). Using liquid chromatography-mass spectrometry-based metabolomics, we screened yeast strains with putative phosphatases of unknown function deleted. We show that the yeast gene YNL010W, which has close homologues in all fungi species and some plants, encodes a sugar alcohol phosphatase. We term this enzyme, which hydrolyzes sorbitol-6-phosphate, ribitol-5-phosphate, and (d)-glycerol-3-phosphate, polyol phosphatase 1 or PYP1. Polyol phosphates are structural analogs of the enediol intermediate of phosphoglucose isomerase (Pgi). We find that sorbitol-6-phosphate and ribitol-5-phosphate inhibit Pgi and that Pyp1 activity is important for yeast to maintain Pgi activity in the presence of environmental sugar alcohols. Pyp1 expression is strongly positively correlated with yeast growth rate, presumably because faster growth requires greater glycolytic and accordingly Pgi flux. Thus, yeast express the previously uncharacterized enzyme Pyp1 to prevent inhibition of glycolysis by sugar alcohol phosphates. Pyp1 may be useful for engineering sugar alcohol production.
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Affiliation(s)
- Yi-Fan Xu
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Wenyun Lu
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
| | - Jonathan C. Chen
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Sarah A. Johnson
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Patrick A. Gibney
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
| | - David G. Thomas
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Amanda L. May
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Shawn R. Campagna
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - David Botstein
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Joshua D. Rabinowitz
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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Emri T, Antal K, Riley R, Karányi Z, Miskei M, Orosz E, Baker S, Wiebenga A, de Vries R, Pócsi I. Duplications and losses of genes encoding known elements of the stress defence system of the Aspergilli contribute to the evolution of these filamentous fungi but do not directly influence their environmental stress tolerance. Stud Mycol 2018; 91:23-36. [PMID: 30425415 PMCID: PMC6231086 DOI: 10.1016/j.simyco.2018.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The contribution of stress protein duplication and deletion events to the evolution of the Aspergilli was studied. We performed a large-scale homology analysis of stress proteins and generated and analysed three stress defence system models based on Saccharomyces cerevisiae, Schizosaccharomyces pombe and Aspergillus nidulans. Although both yeast-based and A. nidulans-based models were suitable to trace evolutionary changes, the A. nidulans-based model performed better in mapping stress protein radiations. The strong Mantel correlation found between the positions of species in the phylogenetic tree on the one hand and either in the A. nidulans-based or S. cerevisiae-based models on the other hand demonstrated that stress protein expansions and reductions contributed significantly to the evolution of the Aspergilli. Interestingly, stress tolerance attributes correlated well with the number of orthologs only for a few stress proteins. Notable examples are Ftr1 iron permease and Fet3 ferro-O2-oxidoreductase, elements of the reductive iron assimilation pathway, in the S. cerevisiae-based model, as well as MpkC, a HogA-like mitogen activated protein kinase in the A. nidulans-based model. In the case of the iron assimilation proteins, the number of orthologs showed a positive correlation with H2O2-induced stress tolerance while the number of MpkC orthologs correlated positively with Congo Red induced cell wall stress, sorbitol induced osmotic stress and H2O2 induced oxidative stress tolerances. For most stress proteins, changes in the number of orthologs did not correlate well with any stress tolerance attributes. As a consequence, stress tolerance patterns of the studied Aspergilli did not correlate with either the sets of stress response proteins in general or with the phylogeny of the species studied. These observations suggest that stress protein duplication and deletion events significantly contributed to the evolution of stress tolerance attributes of Aspergilli. In contrast, there are other processes, which may counterbalance the effects of stress gene duplications or deletions including (i) alterations in the structures of stress proteins leading to changes in their biological activities, (ii) varying biosynthesis of stress proteins, (iii) rewiring stress response regulatory networks or even (iv) acquiring new stress response genes by horizontal gene transfer. All these multilevel changes are indispensable for the successful adaptation of filamentous fungi to altering environmental conditions, especially when these organisms are entering new ecological niches.
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Affiliation(s)
- T. Emri
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032, Debrecen, Hungary
| | - K. Antal
- Department of Zoology, Faculty of Sciences, Eszterházy Károly University, Eszterházy tér 1., H-3300, Eger, Hungary
| | - R. Riley
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Z. Karányi
- Department of Medicine, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, H-4032, Debrecen, Hungary
| | - M. Miskei
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032, Debrecen, Hungary
- MTA-DE Momentum, Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Nagyerdei krt. 98, H-4032, Debrecen, Hungary
| | - E. Orosz
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032, Debrecen, Hungary
| | - S.E. Baker
- Environmental Molecular Sciences Division, Earth and Biological Sciences, Pacific Northwest National Laboratory, Richland, Washington, 99352, USA
| | - A. Wiebenga
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - R.P. de Vries
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - I. Pócsi
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032, Debrecen, Hungary
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25
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Anjago WM, Zhou T, Zhang H, Shi M, Yang T, Zheng H, Wang Z. Regulatory network of genes associated with stimuli sensing, signal transduction and physiological transformation of appressorium in Magnaporthe oryzae. Mycology 2018; 9:211-222. [PMID: 30181927 PMCID: PMC6115909 DOI: 10.1080/21501203.2018.1492981] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/21/2018] [Indexed: 02/02/2023] Open
Abstract
Rice blast caused by Magnaporthe oryzae is the most destructive disease affecting the rice production (Oryza sativa), with an average global loss of 10-30% per annum. Recent reports have indicated that the fungus also inflicts blast disease on wheat (Triticum aestivum) posing a serious threat to the wheat production. Due to its easily detected infectious process and manoeuvrable genetic manipulation, M. oryzae is considered a model organism for exploring the molecular mechanism underlying fungal pathogenicity during the pathogen-host interaction. M. oryzae utilises an infectious structure called appressorium to breach the host surface by generating high turgor pressure. The appressorium development is induced by physical and chemical cues which are coordinated by the highly conserved cAMP/PKA, MAPK and calcium signalling cascades. Genes involved in the appressorium development have been identified and well studied in M. oryzae, a summary of the working gene network linking stimuli sensing and physiological transformation of appressorium is needed. This review provides a comprehensive discussion regarding the regulatory networks underlying appressorium development with particular emphasis on sensing of appressorium inducing stimuli, signal transduction, transcriptional regulation and the corresponding developmental and physiological responses. We also discussed the crosstalk and interaction of various pathways during the appressorium development.
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Affiliation(s)
- Wilfred Mabeche Anjago
- Fujian University Key Laboratory for Plant-Microbe interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tengshen Zhou
- Institute of oceanography, Minjian University, FuzhouChina
| | - Honghong Zhang
- Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mingyue Shi
- Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tao Yang
- Fujian University Key Laboratory for Plant-Microbe interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huakun Zheng
- Fujian University Key Laboratory for Plant-Microbe interaction, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zonghua Wang
- Fujian University Key Laboratory for Plant-Microbe interaction, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of oceanography, Minjian University, FuzhouChina
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26
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Folch-Fortuny A, Teusink B, Hoefsloot HCJ, Smilde AK, Ferrer A. Dynamic elementary mode modelling of non-steady state flux data. BMC SYSTEMS BIOLOGY 2018; 12:71. [PMID: 29914483 PMCID: PMC6006576 DOI: 10.1186/s12918-018-0589-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 05/24/2018] [Indexed: 01/13/2023]
Abstract
BACKGROUND A novel framework is proposed to analyse metabolic fluxes in non-steady state conditions, based on the new concept of dynamic elementary mode (dynEM): an elementary mode activated partially depending on the time point of the experiment. RESULTS Two methods are introduced here: dynamic elementary mode analysis (dynEMA) and dynamic elementary mode regression discriminant analysis (dynEMR-DA). The former is an extension of the recently proposed principal elementary mode analysis (PEMA) method from steady state to non-steady state scenarios. The latter is a discriminant model that permits to identify which dynEMs behave strongly different depending on the experimental conditions. Two case studies of Saccharomyces cerevisiae, with fluxes derived from simulated and real concentration data sets, are presented to highlight the benefits of this dynamic modelling. CONCLUSIONS This methodology permits to analyse metabolic fluxes at early stages with the aim of i) creating reduced dynamic models of flux data, ii) combining many experiments in a single biologically meaningful model, and iii) identifying the metabolic pathways that drive the organism from one state to another when changing the environmental conditions.
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Affiliation(s)
- Abel Folch-Fortuny
- Grupo de Ingeniería Estadística Multivariante, Departamento de Estadística e IO Aplicadas y Calidad, Universitat Politècnica de València, Valencia, Spain. .,Genetics BioIT DBC Department, DSM Food Specialties, Delft, The Netherlands.
| | - Bas Teusink
- Systems Bioinformatics, Centre for Integrative Bioinformatics, Free University of Amsterdam, Amsterdam, The Netherlands
| | - Huub C J Hoefsloot
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Age K Smilde
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Alberto Ferrer
- Grupo de Ingeniería Estadística Multivariante, Departamento de Estadística e IO Aplicadas y Calidad, Universitat Politècnica de València, Valencia, Spain
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27
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MacGilvray ME, Shishkova E, Chasman D, Place M, Gitter A, Coon JJ, Gasch AP. Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response. PLoS Comput Biol 2018; 13:e1006088. [PMID: 29738528 PMCID: PMC5940180 DOI: 10.1371/journal.pcbi.1006088] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 03/13/2018] [Indexed: 11/18/2022] Open
Abstract
Cells respond to stressful conditions by coordinating a complex, multi-faceted response that spans many levels of physiology. Much of the response is coordinated by changes in protein phosphorylation. Although the regulators of transcriptome changes during stress are well characterized in Saccharomyces cerevisiae, the upstream regulatory network controlling protein phosphorylation is less well dissected. Here, we developed a computational approach to infer the signaling network that regulates phosphorylation changes in response to salt stress. We developed an approach to link predicted regulators to groups of likely co-regulated phospho-peptides responding to stress, thereby creating new edges in a background protein interaction network. We then use integer linear programming (ILP) to integrate wild type and mutant phospho-proteomic data and predict the network controlling stress-activated phospho-proteomic changes. The network we inferred predicted new regulatory connections between stress-activated and growth-regulating pathways and suggested mechanisms coordinating metabolism, cell-cycle progression, and growth during stress. We confirmed several network predictions with co-immunoprecipitations coupled with mass-spectrometry protein identification and mutant phospho-proteomic analysis. Results show that the cAMP-phosphodiesterase Pde2 physically interacts with many stress-regulated transcription factors targeted by PKA, and that reduced phosphorylation of those factors during stress requires the Rck2 kinase that we show physically interacts with Pde2. Together, our work shows how a high-quality computational network model can facilitate discovery of new pathway interactions during osmotic stress. Cells sense and respond to stressful environments by utilizing complex signaling networks that integrate diverse signals to coordinate a multi-faceted physiological response. Much of this response is controlled by post-translational protein phosphorylation. Although many regulators that mediate changes in protein phosphorylation are known, how these regulators inter-connect in a single regulatory network that can transmit cellular signals is not known. It is also unclear how regulators that promote growth and regulators that activate the stress response interconnect to reorganize resource allocation during stress. Here, we developed an integrated experimental and computational workflow to infer the signaling network that regulates phosphorylation changes during osmotic stress in the budding yeast Saccharomyces cerevisiae. The workflow integrates data measuring protein phosphorylation changes in response to osmotic stress with known physical interactions between yeast proteins from large-scale datasets, along with other information about how regulators recognize their targets. The resulting network suggested new signaling connections between regulators and pathways, including those involved in regulating growth and defense, and predicted new regulators involved in stress defense. Our work highlights the power of using network inference to deliver new insight on how cells coordinate a diverse adaptive strategy to stress.
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Affiliation(s)
- Matthew E. MacGilvray
- Laboratory of Genetics, University of Wisconsin—Madison, Madison, WI, United States of America
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin—Madison, Madison, WI, United States of America
| | - Deborah Chasman
- Wisconsin Institute for Discovery, University of Wisconsin–Madison, Madison, WI, United States of America
| | - Michael Place
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Anthony Gitter
- Department of Biostatistics and Medical Informatics, University of Wisconsin -Madison, Madison, WI, United States of America
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Joshua J. Coon
- Department of Biomolecular Chemistry, University of Wisconsin—Madison, Madison, WI, United States of America
- Morgridge Institute for Research, Madison, WI, United States of America
- Department of Chemistry, University of Wisconsin -Madison, Madison, WI, United States of America
- Genome Center of Wisconsin, Madison, WI, United States of America
| | - Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin—Madison, Madison, WI, United States of America
- Department of Chemistry, University of Wisconsin -Madison, Madison, WI, United States of America
- * E-mail:
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28
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Jung WH, Son YE, Oh SH, Fu C, Kim HS, Kwak JH, Cardenas ME, Heitman J, Park HS. Had1 Is Required for Cell Wall Integrity and Fungal Virulence in Cryptococcus neoformans. G3 (BETHESDA, MD.) 2018; 8:643-652. [PMID: 29233914 PMCID: PMC5919746 DOI: 10.1534/g3.117.300444] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 12/07/2017] [Indexed: 12/16/2022]
Abstract
Calcineurin modulates environmental stress survival and virulence of the human fungal pathogen Cryptococcus neoformans Previously, we identified 44 putative calcineurin substrates, and proposed that the calcineurin pathway is branched to regulate targets including Crz1, Pbp1, and Puf4 in C. neoformans In this study, we characterized Had1, which is one of the putative calcineurin substrates belonging to the ubiquitously conserved haloacid dehalogenase β-phosphoglucomutase protein superfamily. Growth of the had1∆ mutant was found to be compromised at 38° or higher. In addition, the had1∆ mutant exhibited increased sensitivity to cell wall perturbing agents, including Congo Red and Calcofluor White, and to an endoplasmic reticulum stress inducer dithiothreitol. Virulence studies revealed that the had1 mutation results in attenuated virulence compared to the wild-type strain in a murine inhalation infection model. Genetic epistasis analysis revealed that Had1 and the zinc finger transcription factor Crz1 play roles in parallel pathways that orchestrate stress survival and fungal virulence. Overall, our results demonstrate that Had1 is a key regulator of thermotolerance, cell wall integrity, and virulence of C. neoformans.
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Affiliation(s)
- Won-Hee Jung
- School of Food Science and Biotechnology, Institute of Agricultural Science and Technology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ye-Eun Son
- School of Food Science and Biotechnology, Institute of Agricultural Science and Technology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sang-Hun Oh
- School of Life Science, Handong Global University, Pohang 37554, Republic of Korea
| | - Ci Fu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Hye Shin Kim
- School of Life Science, Handong Global University, Pohang 37554, Republic of Korea
| | - Jin-Hwan Kwak
- School of Life Science, Handong Global University, Pohang 37554, Republic of Korea
| | - Maria E Cardenas
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Hee-Soo Park
- School of Food Science and Biotechnology, Institute of Agricultural Science and Technology, Kyungpook National University, Daegu 41566, Republic of Korea
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Zong H, Liu X, Chen W, Zhuge B, Sun J. Construction of glycerol synthesis pathway in Klebsiella pneumoniae for bioconversion of glucose into 1,3-propanediol. BIOTECHNOL BIOPROC E 2017. [DOI: 10.1007/s12257-016-0375-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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Deep sequencing analysis of transcriptomes in Aspergillus oryzae in response to salinity stress. Appl Microbiol Biotechnol 2017; 102:897-906. [PMID: 29101425 DOI: 10.1007/s00253-017-8603-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 10/09/2017] [Accepted: 10/12/2017] [Indexed: 12/20/2022]
Abstract
Characterization of the changes after various stimuli is crucial to comprehend the adaptation of cells to the changing condition. Aspergillus oryzae is widely used for the industrial production of soy sauce, which always encounter changes within a complex environment, such as salinity stress. However, the protective biochemical mechanisms of A. oryzae against salinity stress are poorly understood. In this study, we successfully characterized the fermentative behavior, transcriptomic profiles, and metabolite changes of A. oryzae in response to salinity stress. The results showed that salt treatment of A. oryzae inhibited the fungal development and conidia formation. Transcriptomic analysis showed an upregulated expression of the genes related to arginine accumulation and oleic acid synthesis. The results of qRT-PCR were further confirmed by the reliability and availability of the differentially expressed genes obtained from the transcriptome analysis. Metabolomic analysis revealed that the corresponding intracellular accumulation of arginine and oleic acid were also increased in response to the salinity stress. All of the results provide a global transcriptome characterization of the salt adaptation process in A. oryzae, and offer multiple target genes for salt tolerance improvement via genetic engineering.
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31
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Glycerol-3-phosphate phosphatase/PGP: Role in intermediary metabolism and target for cardiometabolic diseases. Biochimie 2017; 143:18-28. [PMID: 28826615 DOI: 10.1016/j.biochi.2017.08.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/02/2017] [Indexed: 11/22/2022]
Abstract
Metabolic diseases, including obesity, type 2 diabetes, and metabolic syndrome arise because of disturbances in glucose and fat metabolism, which impact associated physiological events such as insulin secretion and action, fat storage and oxidation. Even though, decades of research has contributed to our current understanding of the components involved in glucose and fat metabolism and their regulation, that led to the development of many therapeutics, there are still many unanswered questions. Glycerol-3-phosphate (Gro3P), which is formed during glycolysis, is at the intersection of glucose and fat metabolism, and the availability of this metabolite can regulate energy and intermediary metabolism in mammalian cells. During the course of evolution, mammalian cells are assumed to have lost the capacity to directly hydrolyze Gro3P to glycerol, until the recent discovery from our laboratory showing that a previously known mammalian enzyme, phosphoglycolate phosphatase (PGP), can function as a Gro3P phosphatase (G3PP) and regulate this metabolite levels. Emerging evidence indicates that G3PP/PGP is an evolutionarily conserved "multi-tasking" enzyme that belongs to the superfamily of haloacid dehalogenase-like phosphatase enzymes, and is capable of hydrolyzing Gro3P, an abundant physiologically relevant substrate, as well as other metabolites including 2-phosphoglycolate, 4-phosphoerythronate and 2-phospholactate, which are present in much smaller amounts in cells, under normal conditions. G3PP, by regulating Gro3P levels, plays a critical role in intermediary metabolism, including glycolysis, glucose oxidation, cellular redox and ATP production, gluconeogenesis, esterification of fatty acids towards glycerolipid synthesis and fatty acid oxidation. Because of G3PP's ability to regulate energy and intermediary metabolism as well as physiological functions such as insulin secretion, hepatic glucose production, and fat synthesis, storage and oxidation, the pathophysiological role of this enzyme in metabolic diseases needs to be precisely defined. In this review, we summarize the present knowledge on the structure, function and regulation of G3PP/PGP, and we discuss its potential therapeutic role for cardiometabolic diseases.
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32
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Xue LL, Chen HH, Jiang JG. Implications of glycerol metabolism for lipid production. Prog Lipid Res 2017; 68:12-25. [PMID: 28778473 DOI: 10.1016/j.plipres.2017.07.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 07/06/2017] [Accepted: 07/31/2017] [Indexed: 12/13/2022]
Abstract
Triacylglycerol (TAG) is an important product in oil-producing organisms. Biosynthesis of TAG can be completed through either esterification of fatty acids to glycerol backbone, or through esterification of 2-monoacylglycerol. This review will focus on the former pathway in which two precursors, fatty acid and glycerol-3-phosphate (G3P), are required for TAG formation. Tremendous progress has been made about the enzymes or genes that regulate the biosynthetic pathway of TAG. However, much attention has been paid to the fatty acid provision and the esterification process, while the possible role of G3P is largely neglected. Glycerol is extensively studied on its usage as carbon source for value-added products, but the modification of glycerol metabolism, which is directly associated with G3P synthesis, is seldom recognized in lipid investigations. The relevance among glycerol metabolism, G3P synthesis and lipid production is described, and the role of G3P in glycerol metabolism and lipid production are discussed in detail with an emphasis on how G3P affects lipid production through the modulation of glycerol metabolism. Observations of lipid metabolic changes due to glycerol related disruption in mammals, plants, and microorganisms are introduced. Altering glycerol metabolism results in the changes of final lipid content. Possible regulatory mechanisms concerning the relationship between glycerol metabolism and lipid production are summarized.
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Affiliation(s)
- Lu-Lu Xue
- (a)College of Food and Bioengineering, South China University of Technology, Guangzhou 510640, China; (b)Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Hao-Hong Chen
- (a)College of Food and Bioengineering, South China University of Technology, Guangzhou 510640, China
| | - Jian-Guo Jiang
- (a)College of Food and Bioengineering, South China University of Technology, Guangzhou 510640, China.
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33
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Schutt KL, Moseley JB. Transient activation of fission yeast AMPK is required for cell proliferation during osmotic stress. Mol Biol Cell 2017; 28:1804-1814. [PMID: 28515144 PMCID: PMC5491188 DOI: 10.1091/mbc.e17-04-0235] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 01/05/2023] Open
Abstract
Transient activation of the cellular energy sensor AMPK during osmotic stress requires its energy-sensing subunit. Cellular ATP levels decrease during osmotic stress, which triggers energy stress, which in turn requires dynamic activation of AMPK. The heterotrimeric kinase AMPK acts as an energy sensor to coordinate cell metabolism with environmental status in species from yeast through humans. Low intracellular ATP leads to AMPK activation through phosphorylation of the activation loop within the catalytic subunit. Other environmental stresses also activate AMPK, but it is unclear whether cellular energy status affects AMPK activation under these conditions. Fission yeast AMPK catalytic subunit Ssp2 is phosphorylated at Thr-189 by the upstream kinase Ssp1 in low-glucose conditions, similar to other systems. Here we find that hyperosmotic stress induces strong phosphorylation of Ssp2-T189 by Ssp1. Ssp2-pT189 during osmotic stress is transient and leads to transient regulation of AMPK targets, unlike sustained activation by low glucose. Cells lacking this activation mechanism fail to proliferate after hyperosmotic stress. Activation during osmotic stress requires energy sensing by AMPK heterotrimer, and osmotic stress leads to decreased intracellular ATP levels. We observed mitochondrial fission during osmotic stress, but blocking fission did not affect AMPK activation. Stress-activated kinases Sty1 and Pmk1 did not promote AMPK activation but contributed to subsequent inactivation. Our results show that osmotic stress induces transient energy stress, and AMPK activation allows cells to manage this energy stress for proliferation in new osmotic states.
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Affiliation(s)
- Katherine L Schutt
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - James B Moseley
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
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Abstract
Adaptation to altered osmotic conditions is a fundamental property of living cells and has been studied in detail in the yeast Saccharomyces cerevisiae. Yeast cells accumulate glycerol as compatible solute, controlled at different levels by the High Osmolarity Glycerol (HOG) response pathway. Up to now, essentially all osmostress studies in yeast have been performed with glucose as carbon and energy source, which is metabolised by glycolysis with glycerol as a by-product. Here we investigated the response of yeast to osmotic stress when yeast is respiring ethanol as carbon and energy source. Remarkably, yeast cells do not accumulate glycerol under these conditions and it appears that trehalose may partly take over the role as compatible solute. The HOG pathway is activated in very much the same way as during growth on glucose and is also required for osmotic adaptation. Slower volume recovery was observed in ethanol-grown cells as compared to glucose-grown cells. Dependence on key regulators as well as the global gene expression profile were similar in many ways to those previously observed in glucose-grown cells. However, there are indications that cells re-arrange redox-metabolism when respiration is hampered under osmostress, a feature that could not be observed in glucose-grown cells.
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Synthetic Biology of Polyhydroxyalkanoates (PHA). ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 162:147-174. [DOI: 10.1007/10_2017_3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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Mizushima D, Iwata H, Ishimaki Y, Ogihara J, Kato J, Kasumi T. Two glycerol 3-phosphate dehydrogenase isogenes from Candida versatilis SN-18 play an important role in glycerol biosynthesis under osmotic stress. J Biosci Bioeng 2016; 121:523-9. [PMID: 26906228 DOI: 10.1016/j.jbiosc.2015.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 09/30/2015] [Accepted: 10/02/2015] [Indexed: 11/17/2022]
Abstract
Two isogenes of glycerol 3-phosphate dehydrogenase (GPD) from Candida versatilis SN-18 were cloned and sequenced. These intronless genes (Cagpd1 and Cagpd2) were both predicted to encode a 378 amino acid polypeptide, and the deduced amino acid sequences mutually showed 76% identity. Interestingly, Cagpd1 and Cagpd2 were located tandemly in a locus of genomic DNA within a 262 bp interval. To our knowledge, this represents a novel instance of isogenic genes relating to glucose metabolism. The stress response element (STRE) was found respectively at -93 to -89 bp upstream of the 5'end of Cagpd1 and -707 to -703 bp upstream of Cagpd2, indicating that these genes are involved in osmotic stress response. In heterologous expression using a gpd1Δgpd2Δ double deletion mutant of Saccharomyces cerevisiae, Cagpd1 and Cagpd2 transformants complemented the function of GPD, with Cagpd2 being much more effective than Cagpd1 in promoting growth and glycerol synthesis. Phylogenetic analysis of the amino acid sequences suggested that Cagpd1p and Cagpd2p are NADP(+)-dependent GPDs (EC 1.1.1.94). However, crude enzyme extract from Cagpd1 and Cagpd2 transformants showed GPD activity with only NAD(+) as cofactor. Hence, both Cagpd1p and Cagpd2p are likely NAD(+)-dependent GPDs (EC 1.1.1.8), similar to GPDs from S. cerevisiae and Candida magnoliae.
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Affiliation(s)
- Daiki Mizushima
- Laboratory of Applied Microbiology and Biotechnology, Department of Chemistry and Lifescience, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Hisashi Iwata
- Laboratory of Applied Microbiology and Biotechnology, Department of Chemistry and Lifescience, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Yuki Ishimaki
- Laboratory of Applied Microbiology and Biotechnology, Department of Chemistry and Lifescience, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Jun Ogihara
- Laboratory of Applied Microbiology and Biotechnology, Department of Chemistry and Lifescience, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Jun Kato
- Laboratory of Applied Microbiology and Biotechnology, Department of Chemistry and Lifescience, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Takafumi Kasumi
- Laboratory of Applied Microbiology and Biotechnology, Department of Chemistry and Lifescience, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan.
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Wang J, Xu R, Wang R, Haque ME, Liu A. Overexpression of ACC gene from oleaginous yeast Lipomyces starkeyi enhanced the lipid accumulation in Saccharomyces cerevisiae with increased levels of glycerol 3-phosphate substrates. Biosci Biotechnol Biochem 2016; 80:1214-22. [PMID: 26865376 DOI: 10.1080/09168451.2015.1136883] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The conversion of acetyl-CoA to malonyl-CoA by acetyl-CoA carboxylase (ACC) is the rate-limiting step in fatty acid biosynthesis. In this study, a gene coding for ACC was isolated and characterized from an oleaginous yeast, Lipomyces starkeyi. Real-time quantitative PCR (qPCR) analysis of L. starkeyi acetyl-CoA carboxylase gene (LsACC1) showed that the expression levels were upregulated with the fast accumulation of lipids. The LsACC1 was co-overexpressed with the glycerol 3-phosphate dehydrogenase gene (GPD1), which regulates lipids biosynthesis by supplying another substrates glycerol 3-phosphate for storage lipid assembly, in the non-oleaginous yeast Saccharomyces cerevisiae. Further, the S. cerevisiae acetyl-CoA carboxylase (ScACC1) was transferred with GPD1 and its function was analyzed in comparison with LsACC1. The results showed that overexpressed LsACC1 and GPD1 resulted in a 63% increase in S. cerevisiae. This study gives new data in understanding of the molecular mechanisms underlying the regulation of fatty acids and lipid biosynthesis in yeasts.
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Affiliation(s)
- Jiancai Wang
- a Key Laboratory of Tropical Plant Resources and Sustainable Use , Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences , Kunming , China.,b School of Life Sciences , University of Science and Technology of China , Hefei , China
| | - Ronghua Xu
- c College of Life Sciences , Anhui Science and Technology University , Fengyang , China
| | - Ruling Wang
- a Key Laboratory of Tropical Plant Resources and Sustainable Use , Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences , Kunming , China
| | - Mohammad Enamul Haque
- d Key Laboratory for Economic Plants and Biotechnology , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming , China
| | - Aizhong Liu
- a Key Laboratory of Tropical Plant Resources and Sustainable Use , Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences , Kunming , China.,d Key Laboratory for Economic Plants and Biotechnology , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming , China
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Identification of a mammalian glycerol-3-phosphate phosphatase: Role in metabolism and signaling in pancreatic β-cells and hepatocytes. Proc Natl Acad Sci U S A 2016; 113:E430-9. [PMID: 26755581 DOI: 10.1073/pnas.1514375113] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Obesity, and the associated disturbed glycerolipid/fatty acid (GL/FA) cycle, contribute to insulin resistance, islet β-cell failure, and type 2 diabetes. Flux through the GL/FA cycle is regulated by the availability of glycerol-3-phosphate (Gro3P) and fatty acyl-CoA. We describe here a mammalian Gro3P phosphatase (G3PP), which was not known to exist in mammalian cells, that can directly hydrolyze Gro3P to glycerol. We identified that mammalian phosphoglycolate phosphatase, with an uncertain function, acts in fact as a G3PP. We found that G3PP, by controlling Gro3P levels, regulates glycolysis and glucose oxidation, cellular redox and ATP production, gluconeogenesis, glycerolipid synthesis, and fatty acid oxidation in pancreatic islet β-cells and hepatocytes, and that glucose stimulated insulin secretion and the response to metabolic stress, e.g., glucolipotoxicity, in β-cells. In vivo overexpression of G3PP in rat liver lowers body weight gain and hepatic glucose production from glycerol and elevates plasma HDL levels. G3PP is expressed at various levels in different tissues, and its expression varies according to the nutritional state in some tissues. As Gro3P lies at the crossroads of glucose, lipid, and energy metabolism, control of its availability by G3PP adds a key level of metabolic regulation in mammalian cells, and G3PP offers a potential target for type 2 diabetes and cardiometabolic disorders.
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Sugar and Glycerol Transport in Saccharomyces cerevisiae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:125-168. [PMID: 26721273 DOI: 10.1007/978-3-319-25304-6_6] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In Saccharomyces cerevisiae the process of transport of sugar substrates into the cell comprises a complex network of transporters and interacting regulatory mechanisms. Members of the large family of hexose (HXT) transporters display uptake efficiencies consistent with their environmental expression and play physiological roles in addition to feeding the glycolytic pathway. Multiple glucose-inducing and glucose-independent mechanisms serve to regulate expression of the sugar transporters in yeast assuring that expression levels and transporter activity are coordinated with cellular metabolism and energy needs. The expression of sugar transport activity is modulated by other nutritional and environmental factors that may override glucose-generated signals. Transporter expression and activity is regulated transcriptionally, post-transcriptionally and post-translationally. Recent studies have expanded upon this suite of regulatory mechanisms to include transcriptional expression fine tuning mediated by antisense RNA and prion-based regulation of transcription. Much remains to be learned about cell biology from the continued analysis of this dynamic process of substrate acquisition.
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Yenush L. Potassium and Sodium Transport in Yeast. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:187-228. [DOI: 10.1007/978-3-319-25304-6_8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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41
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Chu HS, Ahn JH, Yun J, Choi IS, Nam TW, Cho KM. Direct fermentation route for the production of acrylic acid. Metab Eng 2015; 32:23-29. [PMID: 26319589 DOI: 10.1016/j.ymben.2015.08.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 07/30/2015] [Accepted: 08/18/2015] [Indexed: 11/18/2022]
Abstract
There have been growing concerns regarding the limited fossil resources and global climate changes resulting from modern civilization. Currently, finding renewable alternatives to conventional petrochemical processes has become one of the major focus areas of the global chemical industry sector. Since over 4.2 million tons of acrylic acid (AA) is annually employed for the manufacture of various products via petrochemical processes, this chemical has been the target of efforts to replace the petrochemical route by ecofriendly processes. However, there has been limited success in developing an approach combining the biological production of 3-hydroxypropionic acid (3-HP) and its chemical conversion to AA. Here, we report the first direct fermentative route for producing 0.12 g/L of AA from glucose via 3-HP, 3-HP-CoA, and Acryloyl-CoA, leading to a strain of Escherichia coli capable of directly producing acrylic acid. This route was developed through extensive screening of key enzymes and designing a novel metabolic pathway for AA.
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Affiliation(s)
- Hun Su Chu
- Biomaterials Lab, Material Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., 130 Samsung-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, Republic of Korea
| | - Jin-Ho Ahn
- Biomaterials Lab, Material Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., 130 Samsung-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, Republic of Korea
| | - Jiae Yun
- Biomaterials Lab, Material Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., 130 Samsung-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, Republic of Korea
| | - In Suk Choi
- Biomaterials Lab, Material Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., 130 Samsung-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, Republic of Korea
| | - Tae-Wook Nam
- Biomaterials Lab, Material Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., 130 Samsung-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, Republic of Korea
| | - Kwang Myung Cho
- Biomaterials Lab, Material Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., 130 Samsung-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, Republic of Korea.
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42
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Knudsen JD, Johanson T, Eliasson Lantz A, Carlquist M. Exploring the potential of the glycerol-3-phosphate dehydrogenase 2 (GPD2) promoter for recombinant gene expression in Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2015. [PMID: 28626720 PMCID: PMC5466052 DOI: 10.1016/j.btre.2015.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A control point for keeping redox homeostasis in Saccharomyces cerevisiae during fermentative growth is the dynamic regulation of transcription for the glycerol-3-phosphate dehydrogenase 2 (GPD2) gene. In this study, the possibility to steer the activity of the GPD2 promoter was investigated by placing it in strains with different ability to reoxidise NADH, and applying different environmental conditions. Flow cytometric analysis of reporter strains expressing green fluorescent protein (GFP) under the control of the GPD2 promoter was used to determine the promoter activity at the single-cell level. When placed in a gpd1Δgpd2Δ strain background, the GPD2 promoter displayed a 2-fold higher activity as compared to the strong constitutive glyceraldehyde-3-phosphate dehydrogenase (TDH3). In contrast, the GPD2 promoter was found to be inactive when cells were cultivated in continuous mode at a growth rate of 0.3 h−1 and in conditions with excess oxygen (i.e. with an aeration of 2.5 vvm, and a stirring of 800 rpm). In addition, a clear window of operation where the gpd1Δgpd2Δ strain can be grown with the same efficiency as wild type yeast was identified. In conclusion, the flow cytometry mapping revealed conditions where the GPD2 promoter was either completely inactive or hyperactive, which has implications for its implementation in future biotechnological applications such as for process control of heterologous gene expression.
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Affiliation(s)
- Jan Dines Knudsen
- Division of Applied Microbiology, Department of Chemistry, Faculty of Engineering, Lund University, Getingevägen 60, SE-22100 Lund, Sweden
| | - Ted Johanson
- Department of Systems Biology, Technical University of Denmark, Soltofts Plads, Building 223, DK-2800 Kgs. Lyngby, Denmark
| | - Anna Eliasson Lantz
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Soltofts Plads, Building 228, DK-2800 Kgs. Lyngby, Denmark
| | - Magnus Carlquist
- Division of Applied Microbiology, Department of Chemistry, Faculty of Engineering, Lund University, Getingevägen 60, SE-22100 Lund, Sweden
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Kuznetsova E, Nocek B, Brown G, Makarova KS, Flick R, Wolf YI, Khusnutdinova A, Evdokimova E, Jin K, Tan K, Hanson AD, Hasnain G, Zallot R, de Crécy-Lagard V, Babu M, Savchenko A, Joachimiak A, Edwards AM, Koonin EV, Yakunin AF. Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS. J Biol Chem 2015; 290:18678-98. [PMID: 26071590 DOI: 10.1074/jbc.m115.657916] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Indexed: 12/15/2022] Open
Abstract
The haloacid dehalogenase (HAD)-like enzymes comprise a large superfamily of phosphohydrolases present in all organisms. The Saccharomyces cerevisiae genome encodes at least 19 soluble HADs, including 10 uncharacterized proteins. Here, we biochemically characterized 13 yeast phosphatases from the HAD superfamily, which includes both specific and promiscuous enzymes active against various phosphorylated metabolites and peptides with several HADs implicated in detoxification of phosphorylated compounds and pseudouridine. The crystal structures of four yeast HADs provided insight into their active sites, whereas the structure of the YKR070W dimer in complex with substrate revealed a composite substrate-binding site. Although the S. cerevisiae and Escherichia coli HADs share low sequence similarities, the comparison of their substrate profiles revealed seven phosphatases with common preferred substrates. The cluster of secondary substrates supporting significant activity of both S. cerevisiae and E. coli HADs includes 28 common metabolites that appear to represent the pool of potential activities for the evolution of novel HAD phosphatases. Evolution of novel substrate specificities of HAD phosphatases shows no strict correlation with sequence divergence. Thus, evolution of the HAD superfamily combines the conservation of the overall substrate pool and the substrate profiles of some enzymes with remarkable biochemical and structural flexibility of other superfamily members.
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Affiliation(s)
- Ekaterina Kuznetsova
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Boguslaw Nocek
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Greg Brown
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Kira S Makarova
- the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Robert Flick
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Yuri I Wolf
- the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Anna Khusnutdinova
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Elena Evdokimova
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Ke Jin
- the Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada, and
| | - Kemin Tan
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Andrew D Hanson
- the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Ghulam Hasnain
- the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Rémi Zallot
- the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Valérie de Crécy-Lagard
- the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Mohan Babu
- the Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada, and
| | - Alexei Savchenko
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Andrzej Joachimiak
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Aled M Edwards
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada, the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Eugene V Koonin
- the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Alexander F Yakunin
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada,
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Xiao CW, Ji QA, Wei Q, Liu Y, Pan LJ, Bao GL. Digital gene expression analysis of Microsporum canis exposed to berberine chloride. PLoS One 2015; 10:e0124265. [PMID: 25874937 PMCID: PMC4397074 DOI: 10.1371/journal.pone.0124265] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 03/11/2015] [Indexed: 01/23/2023] Open
Abstract
Berberine, a natural isoquinoline alkaloid of many medicinal herbs, has an active function against a variety of microbial infections including Microsporum canis (M. canis). However, the underlying mechanisms are poorly understood. To study the effect of berberine chloride on M. canis infection, a Digital Gene Expression (DGE) tag profiling was constructed and a transcriptome analysis of the M. canis cellular responses upon berberine treatment was performed. Illimina/Hisseq sequencing technique was used to generate the data of gene expression profile, and the following enrichment analysis of Gene Ontology (GO) and Pathway function were conducted based on the data of transcriptome. The results of DGE showed that there were 8476945, 14256722, 7708575, 5669955, 6565513 and 9303468 tags respectively, which was obtained from M. canis incubated with berberine or control DMSO. 8,783 genes were totally mapped, and 1,890 genes have shown significant changes between the two groups. 1,030 genes were up-regulated and 860 genes were down-regulated (P<0.05) in berberine treated group compared to the control group. Besides, twenty-three GO terms were identified by Gene Ontology functional enrichment analysis, such as calcium-transporting ATPase activity, 2-oxoglutarate metabolic process, valine catabolic process, peroxisome and unfolded protein binding. Pathway significant enrichment analysis indicated 6 signaling pathways that are significant, including steroid biosynthesis, steroid hormone biosynthesis, Parkinson’s disease, 2,4-Dichlorobenzoate degradation, and tropane, piperidine and Isoquinoline alkaloid biosynthesis. Among these, eleven selected genes were further verified by qRT-PCR. Our findings provide a comprehensive view on the gene expression profile of M. canis upon berberine treatment, and shed light on its complicated effects on M. canis.
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Affiliation(s)
- Chen-Wen Xiao
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang Province, China
| | - Quan-An Ji
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang Province, China
| | - Qiang Wei
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang Province, China
| | - Yan Liu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang Province, China
| | - Li-Jun Pan
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang Province, China
| | - Guo-Lian Bao
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang Province, China
- * E-mail:
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Vanacloig-Pedros E, Bets-Plasencia C, Pascual-Ahuir A, Proft M. Coordinated gene regulation in the initial phase of salt stress adaptation. J Biol Chem 2015; 290:10163-75. [PMID: 25745106 DOI: 10.1074/jbc.m115.637264] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Indexed: 01/24/2023] Open
Abstract
Stress triggers complex transcriptional responses, which include both gene activation and repression. We used time-resolved reporter assays in living yeast cells to gain insights into the coordination of positive and negative control of gene expression upon salt stress. We found that the repression of "housekeeping" genes coincides with the transient activation of defense genes and that the timing of this expression pattern depends on the severity of the stress. Moreover, we identified mutants that caused an alteration in the kinetics of this transcriptional control. Loss of function of the vacuolar H(+)-ATPase (vma1) or a defect in the biosynthesis of the osmolyte glycerol (gpd1) caused a prolonged repression of housekeeping genes and a delay in gene activation at inducible loci. Both mutants have a defect in the relocation of RNA polymerase II complexes at stress defense genes. Accordingly salt-activated transcription is delayed and less efficient upon partially respiratory growth conditions in which glycerol production is significantly reduced. Furthermore, the loss of Hog1 MAP kinase function aggravates the loss of RNA polymerase II from housekeeping loci, which apparently do not accumulate at inducible genes. Additionally the Def1 RNA polymerase II degradation factor, but not a high pool of nuclear polymerase II complexes, is needed for efficient stress-induced gene activation. The data presented here indicate that the finely tuned transcriptional control upon salt stress is dependent on physiological functions of the cell, such as the intracellular ion balance, the protective accumulation of osmolyte molecules, and the RNA polymerase II turnover.
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Affiliation(s)
- Elena Vanacloig-Pedros
- the Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Carolina Bets-Plasencia
- the Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Amparo Pascual-Ahuir
- the Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Markus Proft
- From the Department of Mechanisms of Plant Stress Responses, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, and
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46
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An integrated view on a eukaryotic osmoregulation system. Curr Genet 2015; 61:373-82. [DOI: 10.1007/s00294-015-0475-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 01/18/2015] [Accepted: 01/19/2015] [Indexed: 10/24/2022]
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47
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Savakis P, Tan X, Du W, Branco dos Santos F, Lu X, Hellingwerf KJ. Photosynthetic production of glycerol by a recombinant cyanobacterium. J Biotechnol 2014; 195:46-51. [PMID: 25541461 DOI: 10.1016/j.jbiotec.2014.12.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/20/2014] [Accepted: 12/11/2014] [Indexed: 10/24/2022]
Abstract
Cyanobacteria are prokaryotic organisms capable of oxygenic photosynthesis. Glycerol is an important commodity chemical. Introduction of phosphoglycerol phosphatase 2 from Saccharomyces cerevisiae into the model cyanobacterium Synechocystis sp. PCC6803 resulted in a mutant strain that produced a considerable amount of glycerol from light, water and COPhotosynthetic production . Mild salt stress (200 mM NaCl) on the cells led to an increase of the extracellular glycerol concentration of more than 20%. Under these conditions the mutant accumulated glycerol to an extracellular concentration of 14.3 mM after 17 days of culturing.
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Affiliation(s)
- Philipp Savakis
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Xiaoming Tan
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, China
| | - Wei Du
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Filipe Branco dos Santos
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, China
| | - Klaas J Hellingwerf
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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48
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Wang M, Dong Y, Zhao Q, Wang F, Liu K, Jiang B, Fang X. Identification of the role of a MAP kinase Tmk2 in Hypocrea jecorina (Trichoderma reesei). Sci Rep 2014; 4:6732. [PMID: 25339247 PMCID: PMC4206845 DOI: 10.1038/srep06732] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 10/02/2014] [Indexed: 12/02/2022] Open
Abstract
Despite the important role of MAPKs in signal transduction, their functions in the cellulase hyper-producing filamentous fungus Hypocrea jecorina haven't been studied except for the Hog1-like Tmk3. In this work, we constructed and explored the features of H. jecorina Δtmk2 to identify the role of this Slt2-homologous Tmk2. It is suggested from the results that Tmk2 is involved in cell wall integrity, sporulation and cellulase production. Although bearing similar roles in cell wall integrity maintenance, Tmk2 and Tmk3 appear to also have distinct functions: Tmk3 participates in high osmolarity resistance while Tmk2 does not; Tmk2 participates in sporulation but not Tmk3; Tmk3 is involved in promoting cellulase production while Tmk2 is involved in repressing cellulase formation. These studies provide the first insight into the function of Tmk2 in H. jecorina and contribute to understanding the signal transduction processes leading to the regulation of cellulase production in this important cellulase hyper-producer.
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Affiliation(s)
- Mingyu Wang
- 1] State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan 250100, China [2] National Glycoengineering Research Center, Shandong University, Jinan 250100, China
| | - Yanmei Dong
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan 250100, China
| | - Qiushuang Zhao
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan 250100, China
| | - Fangzhong Wang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan 250100, China
| | - Kuimei Liu
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan 250100, China
| | - Baojie Jiang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan 250100, China
| | - Xu Fang
- 1] State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan 250100, China [2] National Glycoengineering Research Center, Shandong University, Jinan 250100, China
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Caparrós-Martín JA, McCarthy-Suárez I, Culiáñez-Macià FA. The kinetic analysis of the substrate specificity of motif 5 in a HAD hydrolase-type phosphosugar phosphatase of Arabidopsis thaliana. PLANTA 2014; 240:479-487. [PMID: 24915748 DOI: 10.1007/s00425-014-2102-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 05/16/2014] [Indexed: 06/03/2023]
Abstract
The Arabidopsis thaliana gene AtSgpp (locus tag At2g38740), encodes a protein whose sequence motifs and expected structure reveal that it belongs to the HAD hydrolases subfamily I, with the C1-type cap domain (Caparrós-Martín et al. in Planta 237:943-954, 2013). In the presence of Mg(2+) ions, the enzyme has a phosphatase activity over a wide range of phosphosugar substrates. AtSgpp promiscuity is preferentially detectable on D-ribose-5-phosphate, 2-deoxy-D-ribose-5-phosphate, 2-deoxy-D-glucose-6-phosphate, D-mannose-6-phosphate, D-fructose-1-phosphate, D-glucose-6-phosphate, DL-glycerol-3-phosphate, and D-fructose-6-phosphate. Site-directed mutagenesis analysis of the putative signature sequence motif-5 (IAGKH), which defines its specific chemistry, brings to light the active-site residues Ala-69 and His-72. Mutation A69M, changes the pH dependence of AtSgpp catalysis, and mutant protein AtSgpp-H72K was inactive in phosphomonoester dephosphorylation. It was also observed that substitutions I68M and K71R slightly affect the substrate specificity, while the replacement of the entire motif for that of homologous DL-glycerol-3-phosphatase AtGpp (MMGRK) does not switch AtSgpp activity to the specific targeting for DL-glycerol-3-phosphate.
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Affiliation(s)
- José A Caparrós-Martín
- Instituto de Biología Molecular y Celular de Plantas "Eduardo Primo Yúfera" (UPV-CSIC), Universidad Politécnica de Valencia, Ciudad Politécnica de la Innovación (CPI), C/Ingeniero Fausto Elio s/n, 46022, Valencia, Spain
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50
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Adaptive response and tolerance to sugar and salt stress in the food yeast Zygosaccharomyces rouxii. Int J Food Microbiol 2014; 185:140-57. [DOI: 10.1016/j.ijfoodmicro.2014.05.015] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 04/18/2014] [Accepted: 05/04/2014] [Indexed: 11/21/2022]
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