51
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Gutin J, Joseph‐Strauss D, Sadeh A, Shalom E, Friedman N. Genetic screen of the yeast environmental stress response dynamics uncovers distinct regulatory phases. Mol Syst Biol 2019; 15:e8939. [PMID: 31464369 PMCID: PMC6711295 DOI: 10.15252/msb.20198939] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 07/21/2019] [Accepted: 07/29/2019] [Indexed: 11/09/2022] Open
Abstract
Cells respond to environmental fluctuations by regulating multiple transcriptional programs. This response can be studied by measuring the effect of environmental changes on the transcriptome or the proteome of the cell at the end of the response. However, the dynamics of the response reflect the working of the regulatory mechanisms in action. Here, we utilized a fluorescent stress reporter gene to track the dynamics of protein production in yeast responding to environmental stress. The response is modulated by changes in both the duration and rate of transcription. We probed the underlying molecular pathways controlling these two dimensions using a library of ~1,600 single- and double-mutant strains. Dissection of the effects of these mutants and the interactions between them identified distinct modulators of response duration and response rate. Using a combination of mRNA-seq and live-cell microscopy, we uncover mechanisms by which Msn2/4, Mck1, Msn5, and the cAMP/PKA pathway modulate the response of a large module of stress-induced genes in two discrete regulatory phases. Our results and analysis show that transcriptional stress response is regulated by multiple mechanisms that overlap in time and cellular location.
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Affiliation(s)
- Jenia Gutin
- School of Computer Science and Engineering and Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Daphna Joseph‐Strauss
- School of Computer Science and Engineering and Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Amit Sadeh
- School of Computer Science and Engineering and Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Eli Shalom
- School of Computer Science and Engineering and Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
| | - Nir Friedman
- School of Computer Science and Engineering and Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael
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52
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Rodrigues-Pousada C, Devaux F, Caetano SM, Pimentel C, da Silva S, Cordeiro AC, Amaral C. Yeast AP-1 like transcription factors (Yap) and stress response: a current overview. MICROBIAL CELL 2019; 6:267-285. [PMID: 31172012 PMCID: PMC6545440 DOI: 10.15698/mic2019.06.679] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Yeast adaptation to stress has been extensively studied. It involves large reprogramming of genome expression operated by many, more or less specific, transcription factors. Here, we review our current knowledge on the function of the eight Yap transcription factors (Yap1 to Yap8) in Saccharomyces cerevisiae, which were shown to be involved in various stress responses. More precisely, Yap1 is activated under oxidative stress, Yap2/Cad1 under cadmium, Yap4/Cin5 and Yap6 under osmotic shock, Yap5 under iron overload and Yap8/Arr1 by arsenic compounds. Yap3 and Yap7 seem to be involved in hydroquinone and nitrosative stresses, respectively. The data presented in this article illustrate how much knowledge on the function of these Yap transcription factors is advanced. The evolution of the Yap family and its roles in various pathogenic and non-pathogenic fungal species is discussed in the last section.
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Affiliation(s)
- Claudina Rodrigues-Pousada
- Instituto de Tecnologia Química e Biológica Anónio Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, Oeiras 2781-901, Oeiras, Portugal
| | - Frédéric Devaux
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Soraia M Caetano
- Instituto de Tecnologia Química e Biológica Anónio Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, Oeiras 2781-901, Oeiras, Portugal
| | - Catarina Pimentel
- Instituto de Tecnologia Química e Biológica Anónio Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, Oeiras 2781-901, Oeiras, Portugal
| | - Sofia da Silva
- Instituto de Tecnologia Química e Biológica Anónio Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, Oeiras 2781-901, Oeiras, Portugal
| | - Ana Carolina Cordeiro
- Instituto de Tecnologia Química e Biológica Anónio Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, Oeiras 2781-901, Oeiras, Portugal
| | - Catarina Amaral
- Instituto de Tecnologia Química e Biológica Anónio Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, Oeiras 2781-901, Oeiras, Portugal
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53
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Gier S, Simon M, Nordström K, Khalifa S, Schulz MH, Schmitt MJ, Breinig F. Transcriptome Kinetics of Saccharomyces cerevisiae in Response to Viral Killer Toxin K1. Front Microbiol 2019; 10:1102. [PMID: 31156606 PMCID: PMC6531845 DOI: 10.3389/fmicb.2019.01102] [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: 12/21/2018] [Accepted: 04/30/2019] [Indexed: 11/29/2022] Open
Abstract
The K1 A/B toxin secreted by virus-infected Saccharomyces cerevisiae strains kills sensitive cells via disturbance of cytoplasmic membrane functions. Despite decades of research, the mechanisms underlying K1 toxicity and immunity have not been elucidated yet. In a novel approach, this study aimed to characterize transcriptome changes in K1-treated sensitive yeast cells in a time-dependent manner. Global transcriptional profiling revealed substantial cellular adaptations in target cells resulting in 1,189 differentially expressed genes in total. Killer toxin K1 induced oxidative, cell wall and hyperosmotic stress responses as well as rapid down-regulation of transcription and translation. Essential pathways regulating energy metabolism were also significantly affected by the toxin. Remarkably, a futile cycle of the osmolytes trehalose and glycogen was identified probably representing a critical feature of K1 intoxication. In silico analysis suggested several transcription factors involved in toxin-triggered signal transduction. The identified transcriptome changes provide valuable hints to illuminate the still unknown molecular events leading to K1 toxicity and immunity implicating an evolutionarily conserved response at least initially counteracting ionophoric toxin action.
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Affiliation(s)
- Stefanie Gier
- Department of Molecular and Cell Biology, Saarland University, Saarbrücken, Germany.,Center of Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany
| | - Martin Simon
- Center of Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany.,Molecular Cell Biology and Microbiology, University of Wuppertal, Wuppertal, Germany.,Molecular Cell Dynamics, Saarland University, Saarbrücken, Germany
| | - Karl Nordström
- Center of Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany.,Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Salem Khalifa
- Cluster of Excellence "Multimodal Computing and Interaction", Max Planck Institute for Informatics, Saarland University, Saarbrücken, Germany
| | - Marcel H Schulz
- Cluster of Excellence "Multimodal Computing and Interaction", Max Planck Institute for Informatics, Saarland University, Saarbrücken, Germany
| | - Manfred J Schmitt
- Department of Molecular and Cell Biology, Saarland University, Saarbrücken, Germany.,Center of Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany
| | - Frank Breinig
- Department of Molecular and Cell Biology, Saarland University, Saarbrücken, Germany.,Center of Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken, Germany
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54
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Dose dependent gene expression is dynamically modulated by the history, physiology and age of yeast cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:457-471. [DOI: 10.1016/j.bbagrm.2019.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/21/2019] [Accepted: 02/23/2019] [Indexed: 12/14/2022]
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55
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Improving ethanol yields in sugarcane molasses fermentation by engineering the high osmolarity glycerol pathway while maintaining osmotolerance in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2018; 103:1031-1042. [DOI: 10.1007/s00253-018-9532-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/12/2018] [Accepted: 11/17/2018] [Indexed: 01/10/2023]
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56
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Watcharawipas A, Watanabe D, Takagi H. Sodium Acetate Responses in Saccharomyces cerevisiae and the Ubiquitin Ligase Rsp5. Front Microbiol 2018; 9:2495. [PMID: 30459728 PMCID: PMC6232821 DOI: 10.3389/fmicb.2018.02495] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 09/28/2018] [Indexed: 12/31/2022] Open
Abstract
Recent studies have revealed the feasibility of sodium acetate as a potentially novel inhibitor/stressor relevant to the fermentation from neutralized lignocellulosic hydrolysates. This mini-review focuses on the toxicity of sodium acetate, which is composed of both sodium and acetate ions, and on the involved cellular responses that it elicits, particularly via the high-osmolarity glycerol (HOG) pathway, the Rim101 pathway, the P-type ATPase sodium pumps Ena1/2/5, and the ubiquitin ligase Rsp5 with its adaptors. Increased understanding of cellular responses to sodium acetate would improve our understanding of how cells respond not only to different stimuli but also to composite stresses induced by multiple components (e.g., sodium and acetate) simultaneously. Moreover, unraveling the characteristics of specific stresses under industrially related conditions and the cellular responses evoked by these stresses would be a key factor in the industrial yeast strain engineering toward the increased productivity of not only bioethanol but also advanced biofuels and valuable chemicals that will be in demand in the coming era of bio-based industry.
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Affiliation(s)
- Akaraphol Watcharawipas
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Daisuke Watanabe
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
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57
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The Lsm1-7/Pat1 complex binds to stress-activated mRNAs and modulates the response to hyperosmotic shock. PLoS Genet 2018; 14:e1007563. [PMID: 30059503 PMCID: PMC6085073 DOI: 10.1371/journal.pgen.1007563] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 08/09/2018] [Accepted: 07/15/2018] [Indexed: 12/11/2022] Open
Abstract
RNA-binding proteins (RBPs) establish the cellular fate of a transcript, but an understanding of these processes has been limited by a lack of identified specific interactions between RNA and protein molecules. Using MS2 RNA tagging, we have purified proteins associated with individual mRNA species induced by osmotic stress, STL1 and GPD1. We found members of the Lsm1-7/Pat1 RBP complex to preferentially bind these mRNAs, relative to the non-stress induced mRNAs, HYP2 and ASH1. To assess the functional importance, we mutated components of the Lsm1-7/Pat1 RBP complex and analyzed the impact on expression of osmostress gene products. We observed a defect in global translation inhibition under osmotic stress in pat1 and lsm1 mutants, which correlated with an abnormally high association of both non-stress and stress-induced mRNAs to translationally active polysomes. Additionally, for stress-induced proteins normally triggered only by moderate or high osmostress, in the mutants the protein levels rose high already at weak hyperosmosis. Analysis of ribosome passage on mRNAs through co-translational decay from the 5’ end (5P-Seq) showed increased ribosome accumulation in lsm1 and pat1 mutants upstream of the start codon. This effect was particularly strong for mRNAs induced under osmostress. Thus, our results indicate that, in addition to its role in degradation, the Lsm1-7/Pat1 complex acts as a selective translational repressor, having stronger effect over the translation initiation of heavily expressed mRNAs. Binding of the Lsm1-7/Pat1p complex to osmostress-induced mRNAs mitigates their translation, suppressing it in conditions of weak or no stress, and avoiding a hyperresponse when triggered. When confronted with external physical or chemical stress, cells respond by increasing the mRNA output of a small number of genes required for stress survival, while shutting down the majority of other genes. Moreover, each mRNA is regulated under stress to either enhance or diminish its translation into proteins. The overall purpose is for the cell to optimize gene expression for survival and recovery during rapidly changing conditions. Much of this regulation is mediated by RNA-binding proteins. We have isolated proteins binding to specific mRNAs induced by stress, to investigate how they affect the stress response. We found members of one protein complex to be bound to stress-induced mRNAs. When mutants lacking these proteins were exposed to stress, ribosomes were more engaged with translating mRNAs than in the wild-type. In the mutants, it was also possible to trigger expression of stress proteins with only minimal stress levels. Tracing the passage of ribosomes over mRNAs, we saw that ribosomes accumulated around the start codon in the mutants. These findings indicate that the protein complex is required to moderate the stress response and prevent it from overreacting, which would be harmful for the cell.
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58
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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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59
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Andreu C, Lí Del Olmo M. Biotransformation using halotolerant yeast in seawater: a sustainable strategy to produce R-(-)-phenylacetylcarbinol. Appl Microbiol Biotechnol 2018; 102:4717-4727. [PMID: 29627855 DOI: 10.1007/s00253-018-8945-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 03/02/2018] [Accepted: 03/14/2018] [Indexed: 11/26/2022]
Abstract
Acyloin condensation between benzaldehyde and decarboxylated pyruvate results in the production of R-(-)-phenylacetylcarbinol, a chiral precursor of the drug ephedrine. Huge research efforts have been made to improve the conditions of this reaction and to avoid the generation of by-products. Recently, we reported the advantages of using whole cells of the yeast Debaryomyces etchellsii as biocatalysts for this purpose. In this work, a new strategy, which fulfills green chemistry principles, is proposed and is based on using seawater as a gentle solvent. We demonstrate that, under these conditions, several improvements can be made compared to employing freshwater: (1) the conversion of the starting material in (R)-PAC is higher and with a minimum production of by-products; (2) it is possible to increase at least twofold the benzaldehyde load in the reaction medium; (3) cells can maintain their activity after several recycling rounds, which makes (R)-PAC production an easy and economical process.
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Affiliation(s)
- Cecilia Andreu
- Departament de Química Orgànica, Facultat de Farmàcia, Universitat de València (UVEG), Vicent Andrés Estellés s/n., E-46100, Burjassot, València, Spain.
| | - Marcel Lí Del Olmo
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de València (UVEG), Dr. Moliner 50, E-46100, Burjassot, València, Spain
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60
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Ji H, Lu X, Zong H, Zhuge B. Functional and expression studies of two novel STL1 genes of the osmotolerant and glycerol utilization yeast Candida glycerinogenes. J GEN APPL MICROBIOL 2018; 64:121-126. [PMID: 29607876 DOI: 10.2323/jgam.2017.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Candida glycerinogenes is an osmotolerant yeast used for commercial glycerol production, as well as a glycerol utilization yeast which produces high biomass on glycerol medium. In the present study, two STL1 homologues CgSTL1 and CgSTL2 encoding the putative glycerol transporters were identified, and their products were found to be localized to plasma membranes by tagging GFP protein. The functions of CgSTL1 and CgSTL2 on glycerol transport were confirmed by their expression in S. cerevisiae STL1 null mutant and simultaneous deletion in C. glycerinogenes. The expression of CgSTL1 were osmotic-induced, whereas that of CgSTL2 was constitutive. Over-expression of CgSTL1 and CgSTL2 in C. glycerinogenes resulted in improved glycerol consumption rate and cell growth. Our study provided more details on the glycerol transporter of C. glycerinogenes, the potential cell factory for using glycerol as a carbon source.
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Affiliation(s)
- Hao Ji
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University
| | - Xinyao Lu
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University
| | - Hong Zong
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University
| | - Bin Zhuge
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University
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61
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Ji H, Lu X, Zong H, Zhuge B. γ-aminobutyric acid accumulation enhances the cell growth of Candida glycerinogenes under hyperosmotic conditions. J GEN APPL MICROBIOL 2018. [PMID: 29526924 DOI: 10.2323/jgam.2017.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
γ-aminobutyric acid (GABA) is an important non-protein amino acid involved in the response to various environmental stresses in plant cells. The objectives of this study was to test the hypothesis that intracellular accumulation of GABA improves osmotic tolerance in the unconventional yeast Candida glycerinogenes. In C. glycerinogenes, the expression of UGA4 encoding GABA-specific permease is highly induced by hyperosmotic stress. Exogenous GABA application enhanced intracellular GABA accumulation and promoted cell growth under hyperosmotic conditions. Overexpression of the glutamate decarboxylase gene GAD1 resulted in an increased intracellular GABA and improvement in cell growth under hyperosmotic conditions. These results indicated that improving intracellular GABA accumulation of C. glycerinogenes, either through exogenous application or cellular synthesis, is available for improving the tolerance to hyperosmotic stress. We demonstrate that GABA accumulation plays an important role in osmotic stress resistance of the unconventional yeast C. glycerinogenes.
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Affiliation(s)
- Hao Ji
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University
| | - Xinyao Lu
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University
| | - Hong Zong
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University
| | - Bin Zhuge
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University
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62
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Monteiro B, Ferraz P, Barroca M, da Cruz SH, Collins T, Lucas C. Conditions promoting effective very high gravity sugarcane juice fermentation. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:251. [PMID: 30237826 PMCID: PMC6142328 DOI: 10.1186/s13068-018-1239-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/27/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Applying very high gravity (VHG) fermentation conditions to the sugarcane juice (SCJ) bioethanol industry would improve its environmental and economic sustainability without the need for major infrastructure changes or investments. It could enable a decrease in the consumption of biological and natural resources (cane/land, water and energy) while maintaining acceptable production parameters. The present study attempts to demonstrate and characterise an effective industrially relevant SCJ-VHG fermentation process. RESULTS An industry-like SCJ-VHG bioethanol production process with 30 and 35 °Bx broth was employed to investigate the effects of both the yeast strain used and nitrogen source supplementation on process yield, process productivity, biomass viability, glycerol concentration and retention-associated gene expression. Process performance was shown to be variably affected by the different process conditions investigated. Highest process efficiency, with a 17% (w/v) ethanol yield and only 0.2% (w/v) sugar remaining unfermented, was observed with the Saccharomyces cerevisiae industrial strain CAT-1 in 30 °Bx broth with urea supplementation. In addition, efficient retention of glycerol by the yeast strain was identified as a requisite for better fermentation and was consistent with a higher expression of glycerol permease STL1 and channel FPS1. Urea was shown to promote the deregulation of STL1 expression, overcoming glucose repression. The consistency between Fps1-mediated ethanol secretion and ethanol in the extracellular media reinforces previous suggestions that ethanol might exit the cell through the Fps1 channel. CONCLUSIONS This work brings solid evidence in favour of the utilisation of VHG conditions in SCJ fermentations, bringing it a step closer to industrial application. SCJ concentrated up to 30 °Bx maintains industrially relevant ethanol production yield and productivity, provided the broth is supplemented with a suitable nitrogen source and an appropriate industrial bioethanol-producing yeast strain is used. In addition, the work contributes to a better understanding of the VHG-SCJ process and the variable effects of process parameters on process efficiency and yeast strain response.
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Affiliation(s)
- Bruno Monteiro
- Laboratory of Food and Beverage Biotechnology, ESALQ, University of São Paulo, Piracicaba, SP 13418-900 Brazil
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, 4710-057 Braga, Portugal
| | - Pedro Ferraz
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S)/CBMA, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Mário Barroca
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S)/CBMA, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Sandra H. da Cruz
- Laboratory of Food and Beverage Biotechnology, ESALQ, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | - Tony Collins
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S)/CBMA, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Cândida Lucas
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, 4710-057 Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S)/CBMA, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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63
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Nagy G, Szebenyi C, Csernetics Á, Vaz AG, Tóth EJ, Vágvölgyi C, Papp T. Development of a plasmid free CRISPR-Cas9 system for the genetic modification of Mucor circinelloides. Sci Rep 2017; 7:16800. [PMID: 29196656 PMCID: PMC5711797 DOI: 10.1038/s41598-017-17118-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/22/2017] [Indexed: 12/31/2022] Open
Abstract
Mucor circinelloides and other members of Mucorales are filamentous fungi, widely used as model organisms in basic and applied studies. Although genetic manipulation methods have been described for some Mucoral fungi, construction of stable integrative transformants by homologous recombination has remained a great challenge in these organisms. In the present study, a plasmid free CRISPR-Cas9 system was firstly developed for the genetic modification of a Mucoral fungus. The described method offers a rapid but robust tool to obtain mitotically stable mutants of M. circinelloides via targeted integration of the desired DNA. It does not require plasmid construction and its expression in the recipient organism. Instead, it involves the direct introduction of the guide RNA and the Cas9 enzyme and, in case of homology directed repair (HDR), the template DNA into the recipient strain. Efficiency of the method for non-homologous end joining (NHEJ) and HDR was tested by disrupting two different genes, i.e. carB encoding phytoene dehydrogenase and hmgR2 encoding 3-hydroxy-3-methylglutaryl-CoA reductase, of M. circinelloides. Both NHEJ and HDR resulted in stable gene disruption mutants. While NHEJ caused extensive deletions upstream from the protospacer adjacent motif, HDR assured the integration of the deletion cassette at the targeted site.
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Affiliation(s)
- Gábor Nagy
- MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Hungarian Academy of Sciences - University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary
| | - Csilla Szebenyi
- MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Hungarian Academy of Sciences - University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary
| | - Árpád Csernetics
- MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Hungarian Academy of Sciences - University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary
| | - Amanda Grace Vaz
- MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Hungarian Academy of Sciences - University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary
| | - Eszter Judit Tóth
- MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Hungarian Academy of Sciences - University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary
| | - Tamás Papp
- MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Hungarian Academy of Sciences - University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary.
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726, Szeged, Hungary.
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64
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Wu G, Xu Z, Jönsson LJ. Profiling of Saccharomyces cerevisiae transcription factors for engineering the resistance of yeast to lignocellulose-derived inhibitors in biomass conversion. Microb Cell Fact 2017; 16:199. [PMID: 29137634 PMCID: PMC5686817 DOI: 10.1186/s12934-017-0811-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 11/04/2017] [Indexed: 11/24/2022] Open
Abstract
Background Yeast transcription factors (TFs) involved in the regulation of multidrug resistance (MDR) were investigated in experiments with deletion mutants, transformants overexpressing synthetic genes encoding TFs, and toxic concentrations of lignocellulose-derived substances added to cultures as complex mixtures or as specific compounds, viz. coniferyl aldehyde, 5-hydroxymethylfurfural, and furfural. Results In the presence of complex mixtures of toxic substances from spruce wood, transformants overexpressing YAP1 and STB5, TFs involved in oxidative stress response, exhibited enhanced relative growth rates amounting to 4.589 ± 0.261 and 1.455 ± 0.185, respectively. Other TFs identified as important for resistance included DAL81, GZF3, LEU3, PUT3, and WAR1. Potential overlapping functions of YAP1 and STB5 were investigated in experiments with permutations of deletions and overexpression of the two genes. YAP1 complemented STB5 with respect to resistance to 5-hydroxymethylfurfural, but had a distinct role with regard to resistance to coniferyl aldehyde as deletion of YAP1 rendered the cell incapable of resisting coniferyl aldehyde even if STB5 was overexpressed. Conclusions We have investigated 30 deletion mutants and eight transformants overexpressing MDR transcription factors with regard to the roles the transcription factors play in the resistance to toxic concentrations of lignocellulose-derived substances. This work provides an overview of the involvement of thirty transcription factors in the resistance to lignocellulose-derived substances, shows distinct and complementary roles played by YAP1 and STB5, and offers directions for the engineering of robust yeast strains for fermentation processes based on lignocellulosic feedstocks.![]() Electronic supplementary material The online version of this article (10.1186/s12934-017-0811-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guochao Wu
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden.
| | - Zixiang Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Leif J Jönsson
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
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65
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Li X, Yang Y, Zhan C, Zhang Z, Liu X, Liu H, Bai Z. Transcriptional analysis of impacts of glycerol transporter 1 on methanol and glycerol metabolism in Pichia pastoris. FEMS Yeast Res 2017; 18:4582313. [DOI: 10.1093/femsyr/fox081] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/29/2017] [Indexed: 01/13/2023] Open
Affiliation(s)
- Xiang Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Yankun Yang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Chunjun Zhan
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhenyang Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Xiuxia Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Hebin Liu
- Department of Biological Science, Xi’an Jiaotong-Liverpool University, 111 Ren’ai Road, Suzhou 215123, China
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
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66
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Impact of Glucose Concentration and NaCl Osmotic Stress on Yeast Cell Wall β-d-Glucan Formation during Anaerobic Fermentation Process. FERMENTATION-BASEL 2017. [DOI: 10.3390/fermentation3030044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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67
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Zhu M, Fan W, Cha Y, Yang X, Lai Z, Li S, Wang X. Dynamic cell responses in Thermoanaerobacterium sp. under hyperosmotic stress. Sci Rep 2017; 7:10088. [PMID: 28855699 PMCID: PMC5577258 DOI: 10.1038/s41598-017-10514-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/09/2017] [Indexed: 12/17/2022] Open
Abstract
As a nongenetic engineering technique, adaptive evolution is an effective and easy-to-operate approach to strain improvement. In this work, a commercial Thermoanaerobacterium aotearoense SCUT27/Δldh-G58 was successfully isolated via sequential batch fermentation with step-increased carbon concentrations. Mutants were isolated under selective high osmotic pressures for 58 passages. The evolved isolate rapidly catabolized sugars at high concentrations and subsequently produced ethanol with good yield. A 1.6-fold improvement of ethanol production was achieved in a medium containing 120 g/L of carbon substrate using the evolved strain, compared to the start strain. The analysis of transcriptome and intracellular solute pools suggested that the adaptive evolution altered the synthesis of some compatible solutes and activated the DNA repair system in the two Thermoanaerobacterium sp. evolved strains. Overall, the results indicated the potential of adaptive evolution as a simple and effective tool for the modification and optimization of industrial microorganisms.
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Affiliation(s)
- Muzi Zhu
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Wudi Fan
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yaping Cha
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiaofeng Yang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zhicheng Lai
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shuang Li
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.
| | - Xiaoning Wang
- State Key Laboratory of Kidney, the Institute of Life Sciences, Chinese PLA General Hospital, Beijing, China
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68
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Chang YL, Tseng SF, Huang YC, Shen ZJ, Hsu PH, Hsieh MH, Yang CW, Tognetti S, Canal B, Subirana L, Wang CW, Chen HT, Lin CY, Posas F, Teng SC. Yeast Cip1 is activated by environmental stress to inhibit Cdk1-G1 cyclins via Mcm1 and Msn2/4. Nat Commun 2017; 8:56. [PMID: 28676626 PMCID: PMC5496861 DOI: 10.1038/s41467-017-00080-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 06/01/2017] [Indexed: 12/20/2022] Open
Abstract
Upon environmental changes, proliferating cells delay cell cycle to prevent further damage accumulation. Yeast Cip1 is a Cdk1 and Cln2-associated protein. However, the function and regulation of Cip1 are still poorly understood. Here we report that Cip1 expression is co-regulated by the cell-cycle-mediated factor Mcm1 and the stress-mediated factors Msn2/4. Overexpression of Cip1 arrests cell cycle through inhibition of Cdk1–G1 cyclin complexes at G1 stage and the stress-activated protein kinase-dependent Cip1 T65, T69, and T73 phosphorylation may strengthen the Cip1and Cdk1–G1 cyclin interaction. Cip1 accumulation mainly targets Cdk1–Cln3 complex to prevent Whi5 phosphorylation and inhibit early G1 progression. Under osmotic stress, Cip1 expression triggers transient G1 delay which plays a functionally redundant role with another hyperosmolar activated CKI, Sic1. These findings indicate that Cip1 functions similarly to mammalian p21 as a stress-induced CDK inhibitor to decelerate cell cycle through G1 cyclins to cope with environmental stresses. A G1 cell cycle regulatory kinase Cip1 has been identified in budding yeast but how this is regulated is unclear. Here the authors identify cell cycle (Mcm1) and stress-mediated (Msn 2/4) transcription factors as regulating Cip1, causing stress induced CDK inhibition and delay in cell cycle progression.
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Affiliation(s)
- Ya-Lan Chang
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Shun-Fu Tseng
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan.,Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, 11490, Taiwan
| | - Yu-Ching Huang
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Zih-Jie Shen
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Pang-Hung Hsu
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, 20224, Taiwan
| | - Meng-Hsun Hsieh
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Chia-Wei Yang
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Silvia Tognetti
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, 08003, Spain
| | - Berta Canal
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, 08003, Spain
| | - Laia Subirana
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, 08003, Spain
| | - Chien-Wei Wang
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Hsiao-Tan Chen
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Chi-Ying Lin
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Francesc Posas
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, 08003, Spain
| | - Shu-Chun Teng
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan.
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69
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Brown AJP, Cowen LE, di Pietro A, Quinn J. Stress Adaptation. Microbiol Spectr 2017; 5:10.1128/microbiolspec.FUNK-0048-2016. [PMID: 28721857 PMCID: PMC5701650 DOI: 10.1128/microbiolspec.funk-0048-2016] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Indexed: 01/21/2023] Open
Abstract
Fungal species display an extraordinarily diverse range of lifestyles. Nevertheless, the survival of each species depends on its ability to sense and respond to changes in its natural environment. Environmental changes such as fluctuations in temperature, water balance or pH, or exposure to chemical insults such as reactive oxygen and nitrogen species exert stresses that perturb cellular homeostasis and cause molecular damage to the fungal cell. Consequently, fungi have evolved mechanisms to repair this damage, detoxify chemical insults, and restore cellular homeostasis. Most stresses are fundamental in nature, and consequently, there has been significant evolutionary conservation in the nature of the resultant responses across the fungal kingdom and beyond. For example, heat shock generally induces the synthesis of chaperones that promote protein refolding, antioxidants are generally synthesized in response to an oxidative stress, and osmolyte levels are generally increased following a hyperosmotic shock. In this article we summarize the current understanding of these and other stress responses as well as the signaling pathways that regulate them in the fungi. Model yeasts such as Saccharomyces cerevisiae are compared with filamentous fungi, as well as with pathogens of plants and humans. We also discuss current challenges associated with defining the dynamics of stress responses and with the elaboration of fungal stress adaptation under conditions that reflect natural environments in which fungal cells may be exposed to different types of stresses, either sequentially or simultaneously.
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Affiliation(s)
- Alistair J P Brown
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Aberdeen Fungal Group, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Antonio di Pietro
- Departamento de Genética, Universidad de Córdoba, Campus de Rabanales, Edificio Gregor Mendel C5, 14071 Córdoba, Spain
| | - Janet Quinn
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
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70
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Ask yeast how to burn your fats: lessons learned from the metabolic adaptation to salt stress. Curr Genet 2017. [DOI: 10.1007/s00294-017-0724-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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71
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Shellhammer JP, Morin-Kensicki E, Matson JP, Yin G, Isom DG, Campbell SL, Mohney RP, Dohlman HG. Amino acid metabolites that regulate G protein signaling during osmotic stress. PLoS Genet 2017; 13:e1006829. [PMID: 28558063 PMCID: PMC5469498 DOI: 10.1371/journal.pgen.1006829] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/13/2017] [Accepted: 05/17/2017] [Indexed: 12/29/2022] Open
Abstract
All cells respond to osmotic stress by implementing molecular signaling events to protect the organism. Failure to properly adapt can lead to pathologies such as hypertension and ischemia-reperfusion injury. Mitogen-activated protein kinases (MAPKs) are activated in response to osmotic stress, as well as by signals acting through G protein-coupled receptors (GPCRs). For proper adaptation, the action of these kinases must be coordinated. To identify second messengers of stress adaptation, we conducted a mass spectrometry-based global metabolomics profiling analysis, quantifying nearly 300 metabolites in the yeast S. cerevisiae. We show that three branched-chain amino acid (BCAA) metabolites increase in response to osmotic stress and require the MAPK Hog1. Ectopic addition of these BCAA derivatives promotes phosphorylation of the G protein α subunit and dampens G protein-dependent transcription, similar to that seen in response to osmotic stress. Conversely, genetic ablation of Hog1 activity or the BCAA-regulatory enzymes leads to diminished phosphorylation of Gα and increased transcription. Taken together, our results define a new class of candidate second messengers that mediate cross talk between osmotic stress and GPCR signaling pathways.
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Affiliation(s)
- James P. Shellhammer
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | | | - Jacob P. Matson
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Guowei Yin
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Daniel G. Isom
- The University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Sharon L. Campbell
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Robert P. Mohney
- Metabolon, Inc., Research Triangle Park, North Carolina, United States of America
| | - Henrik G. Dohlman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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72
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Bloom ALM, Leipheimer J, Panepinto JC. mRNA decay: an adaptation tool for the environmental fungal pathogen Cryptococcus neoformans. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28524625 DOI: 10.1002/wrna.1424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 12/22/2022]
Abstract
Fungi are ubiquitous in the environment and humans constantly encounter them in the soil, air, water, and food. The vast majority of these interactions are inconsequential. However, in the context of immunodeficiency precipitated by HIV infection, hematologic malignancy, or transplantation, a small subset of fungi can cause devastating, systemic infection. The most deadly of the opportunistic environmental fungi, Cryptococcus neoformans, is estimated to cause hundreds of thousands of deaths per year, mostly in the context of HIV co-infection. The cellular processes that mediate adaptation to the host environment are of great interest as potential novel therapeutic targets. One such cellular process important for host adaptation is mRNA decay, which mediates the specific degradation of subsets of functionally related mRNAs in response to stressors relevant to pathogenesis, including human core body temperature, carbon limitation, and reactive oxygen stress. Thus, for C. neoformans, host adaptation requires mRNA decay to mediate rapid transcriptome remodeling in the face of stressors encountered in the host. Several nodes of stress-responsive signaling that govern the stress-responsive transcriptome also control the decay rate of mRNAs cleared from the ribosome during stress, suggesting an additional layer of coupling between mRNA synthesis and decay that allows C. neoformans to be a successful pathogen of humans. WIREs RNA 2017, 8:e1424. doi: 10.1002/wrna.1424 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Amanda L M Bloom
- Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Jay Leipheimer
- Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - John C Panepinto
- Witebsky Center for Microbial Pathogenesis and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
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73
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Ji H, Lu X, Zong H, Zhuge B. A synthetic hybrid promoter for D-xylonate production at low pH in the tolerant yeast Candida glycerinogenes. Bioengineered 2017; 8:700-706. [PMID: 28471311 DOI: 10.1080/21655979.2017.1312229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The tolerant yeast Candida glycerinogenes, with high D-xylonate and low-pH tolerances, was used as the host for D-xylonate production at low pH in this study. A low-pH inducible promoter, pGUKd, was engineered using the core promoter of the glyceraldehyde-3-phosphate dehydrogenase gene (pGAP) combined with the upstream activating sequence of the promoter of the guanylate kinase gene (pGUK1) that had substituted pH-responsive TF binding sites. The recombinant cells that expressed GFP from the hybrid promoter pGUKd displayed dramatically increased fluorescence intensity at pH 2.5, thus verifying that pGUKd is a low-pH inducible promoter. The promoter pGUKd was then used to express the D-xylose dehydrogenase gene xylB, resulting in increased expression levels of xylB at low pH. The recombinant protein exhibited higher specific activities under lower pH conditions and produced 38 g/l D-xylonate at pH 2.5. This rate is much higher than that produced by fermentation at pH 5.5. These results suggest that the novel hybrid promoter pGUKd functions to direct the production of D-xylonate at low pH, and we provide a candidate genetic tool for the stress tolerant yeast C. glycerinogenes.
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Affiliation(s)
- Hao Ji
- a The Key Laboratory of Carbohydrate Chemistry and Biotechnology , Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology , Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China
| | - Xinyao Lu
- a The Key Laboratory of Carbohydrate Chemistry and Biotechnology , Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology , Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China
| | - Hong Zong
- a The Key Laboratory of Carbohydrate Chemistry and Biotechnology , Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology , Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China
| | - Bin Zhuge
- a The Key Laboratory of Carbohydrate Chemistry and Biotechnology , Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology , Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China
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Salas-Delgado G, Ongay-Larios L, Kawasaki-Watanabe L, López-Villaseñor I, Coria R. The yeasts phosphorelay systems: a comparative view. World J Microbiol Biotechnol 2017; 33:111. [PMID: 28470426 DOI: 10.1007/s11274-017-2272-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/25/2017] [Indexed: 12/23/2022]
Abstract
Cells contain signal transduction pathways that mediate communication between the extracellular environment and the cell interior. These pathways control transcriptional programs and posttranscriptional processes that modify cell metabolism in order to maintain homeostasis. One type of these signal transduction systems are the so-called Two Component Systems (TCS), which conduct the transfer of phosphate groups between specific and conserved histidine and aspartate residues present in at least two proteins; the first protein is a sensor kinase which autophosphorylates a histidine residue in response to a stimulus, this phosphate is then transferred to an aspartic residue located in a response regulator protein. There are classical and hybrid TCS, whose difference consists in the number of proteins and functional domains involved in the phosphorelay. The TCS are widespread in bacteria where the sensor and its response regulator are mostly specific for a given stimulus. In eukaryotic organisms such as fungi, slime molds, and plants, TCS are present as hybrid multistep phosphorelays, with a variety of arrangements (Stock et al. in Annu Rev Biochem 69:183-215, 2000; Wuichet et al. in Curr Opin Microbiol 292:1039-1050, 2010). In these multistep phosphorelay systems, several phosphotransfer events take place between different histidine and aspartate residues localized in specific domains present in more than two proteins (Thomason and Kay, in J Cell Sci 113:3141-3150, 2000; Robinson et al. in Nat Struct Biol 7:626-633, 2000). This review presents a brief and succinct description of the Two-component systems of model yeasts, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans, Cryptococcus neoformans and Kluyveromyces lactis. We have focused on the comparison of domain organization and functions of each component present in these phosphorelay systems.
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Affiliation(s)
- Griselda Salas-Delgado
- Departamento de Genética Molecular, Instituto de FisiologíaCelular, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Laura Ongay-Larios
- Unidad de Biología Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Laura Kawasaki-Watanabe
- Departamento de Genética Molecular, Instituto de FisiologíaCelular, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Imelda López-Villaseñor
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Roberto Coria
- Departamento de Genética Molecular, Instituto de FisiologíaCelular, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México.
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75
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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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76
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Auesukaree C. Molecular mechanisms of the yeast adaptive response and tolerance to stresses encountered during ethanol fermentation. J Biosci Bioeng 2017; 124:133-142. [PMID: 28427825 DOI: 10.1016/j.jbiosc.2017.03.009] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/16/2017] [Indexed: 12/28/2022]
Abstract
During ethanol fermentation, yeast cells encounter various stresses including sugar substrates-induced high osmolarity, increased ethanol concentration, oxygen metabolism-derived reactive oxygen species (ROS), and elevated temperature. To cope with these fermentation-associated stresses, appropriate adaptive responses are required to prevent stress-induced cellular dysfunctions and to acquire stress tolerances. This review will focus on the cellular effects of these stresses, molecular basis of the adaptive response to each stress, and the cellular mechanisms contributing to stress tolerance. Since a single stress can cause diverse effects, including specific and non-specific effects, both specific and general stress responses are needed for achieving comprehensive protection. For instance, the high-osmolarity glycerol (HOG) pathway and the Yap1/Skn7-mediated pathways are specifically involved in responses to osmotic and oxidative stresses, respectively. On the other hand, due to the common effect of these stresses on disturbing protein structures, the upregulation of heat shock proteins (HSPs) and trehalose is induced upon exposures to all of these stresses. A better understanding of molecular mechanisms underlying yeast tolerance to these fermentation-associated stresses is essential for improvement of yeast stress tolerance by genetic engineering approaches.
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Affiliation(s)
- Choowong Auesukaree
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok 10400, Thailand.
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77
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Manzanares-Estreder S, Espí-Bardisa J, Alarcón B, Pascual-Ahuir A, Proft M. Multilayered control of peroxisomal activity upon salt stress in Saccharomyces cerevisiae. Mol Microbiol 2017; 104:851-868. [PMID: 28321934 DOI: 10.1111/mmi.13669] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2017] [Indexed: 02/02/2023]
Abstract
Peroxisomes are dynamic organelles and the sole location for fatty acid β-oxidation in yeast cells. Here, we report that peroxisomal function is crucial for the adaptation to salt stress, especially upon sugar limitation. Upon stress, multiple layers of control regulate the activity and the number of peroxisomes. Activated Hog1 MAP kinase triggers the induction of genes encoding enzymes for fatty acid activation, peroxisomal import and β-oxidation through the Adr1 transcriptional activator, which transiently associates with genes encoding fatty acid metabolic enzymes in a stress- and Hog1-dependent manner. Moreover, Na+ and Li+ stress increases the number of peroxisomes per cell in a Hog1-independent manner, which depends instead of the retrograde pathway and the dynamin related GTPases Dnm1 and Vps1. The strong activation of the Faa1 fatty acyl-CoA synthetase, which specifically localizes to lipid particles and peroxisomes, indicates that adaptation to salt stress requires the enhanced mobilization of fatty acids from internal lipid stores. Furthermore, the activation of mitochondrial respiration during stress depends on peroxisomes, mitochondrial acetyl-carnitine uptake is essential for salt resistance and the number of peroxisomes attached to the mitochondrial network increases during salt adaptation, which altogether indicates that stress-induced peroxisomal β-oxidation triggers enhanced respiration upon salt shock.
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Affiliation(s)
- Sara Manzanares-Estreder
- Instituto de Biomedicina de Valencia IBV-CSIC, Department of Molecular and Cellular Pathology and Therapy, Jaime Roig 11, Valencia, 46010, Spain.,Instituto de Biología Molecular y Celular de Plantas, CSIC-Universitat Politècnica de València, Ciudad Politécnica de la Innovación, Department of Biotechnology, Edificio 8E, Ingeniero Fausto Elio s/n, Valencia, 46022, Spain
| | - Joan Espí-Bardisa
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universitat Politècnica de València, Ciudad Politécnica de la Innovación, Department of Biotechnology, Edificio 8E, Ingeniero Fausto Elio s/n, Valencia, 46022, Spain
| | - Benito Alarcón
- Instituto de Biomedicina de Valencia IBV-CSIC, Department of Molecular and Cellular Pathology and Therapy, Jaime Roig 11, Valencia, 46010, Spain
| | - Amparo Pascual-Ahuir
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universitat Politècnica de València, Ciudad Politécnica de la Innovación, Department of Biotechnology, Edificio 8E, Ingeniero Fausto Elio s/n, Valencia, 46022, Spain
| | - Markus Proft
- Instituto de Biomedicina de Valencia IBV-CSIC, Department of Molecular and Cellular Pathology and Therapy, Jaime Roig 11, Valencia, 46010, Spain
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78
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Belda I, Ruiz J, Alonso A, Marquina D, Santos A. The Biology of Pichia membranifaciens Killer Toxins. Toxins (Basel) 2017; 9:toxins9040112. [PMID: 28333108 PMCID: PMC5408186 DOI: 10.3390/toxins9040112] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/07/2017] [Accepted: 03/20/2017] [Indexed: 02/07/2023] Open
Abstract
The killer phenomenon is defined as the ability of some yeast to secrete toxins that are lethal to other sensitive yeasts and filamentous fungi. Since the discovery of strains of Saccharomyces cerevisiae capable of secreting killer toxins, much information has been gained regarding killer toxins and this fact has substantially contributed knowledge on fundamental aspects of cell biology and yeast genetics. The killer phenomenon has been studied in Pichia membranifaciens for several years, during which two toxins have been described. PMKT and PMKT2 are proteins of low molecular mass that bind to primary receptors located in the cell wall structure of sensitive yeast cells, linear (1→6)-β-d-glucans and mannoproteins for PMKT and PMKT2, respectively. Cwp2p also acts as a secondary receptor for PMKT. Killing of sensitive cells by PMKT is characterized by ionic movements across plasma membrane and an acidification of the intracellular pH triggering an activation of the High Osmolarity Glycerol (HOG) pathway. On the contrary, our investigations showed a mechanism of killing in which cells are arrested at an early S-phase by high concentrations of PMKT2. However, we concluded that induced mortality at low PMKT2 doses and also PMKT is indeed of an apoptotic nature. Killer yeasts and their toxins have found potential applications in several fields: in food and beverage production, as biocontrol agents, in yeast bio-typing, and as novel antimycotic agents. Accordingly, several applications have been found for P. membranifaciens killer toxins, ranging from pre- and post-harvest biocontrol of plant pathogens to applications during wine fermentation and ageing (inhibition of Botrytis cinerea, Brettanomyces bruxellensis, etc.).
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Affiliation(s)
- Ignacio Belda
- Department of Microbiology, Biology Faculty, Complutense University of Madrid, 28040 Madrid, Spain.
| | - Javier Ruiz
- Department of Microbiology, Biology Faculty, Complutense University of Madrid, 28040 Madrid, Spain.
| | - Alejandro Alonso
- Department of Microbiology, Biology Faculty, Complutense University of Madrid, 28040 Madrid, Spain.
| | - Domingo Marquina
- Department of Microbiology, Biology Faculty, Complutense University of Madrid, 28040 Madrid, Spain.
| | - Antonio Santos
- Department of Microbiology, Biology Faculty, Complutense University of Madrid, 28040 Madrid, Spain.
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79
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An mRNA decapping mutant deficient in P body assembly limits mRNA stabilization in response to osmotic stress. Sci Rep 2017; 7:44395. [PMID: 28290514 PMCID: PMC5349606 DOI: 10.1038/srep44395] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/07/2017] [Indexed: 01/19/2023] Open
Abstract
Yeast is exposed to changing environmental conditions and must adapt its genetic program to provide a homeostatic intracellular environment. An important stress for yeast in the wild is high osmolarity. A key response to this stress is increased mRNA stability primarily by the inhibition of deadenylation. We previously demonstrated that mutations in decapping activators (edc3∆ lsm4∆C), which result in defects in P body assembly, can destabilize mRNA under unstressed conditions. We wished to examine whether mRNA would be destabilized in the edc3∆ lsm4∆C mutant as compared to the wild-type in response to osmotic stress, when P bodies are intense and numerous. Our results show that the edc3∆ lsm4∆C mutant limits the mRNA stability in response to osmotic stress, while the magnitude of stabilization was similar as compared to the wild-type. The reduced mRNA stability in the edc3∆ lsm4∆C mutant was correlated with a shorter PGK1 poly(A) tail. Similarly, the MFA2 mRNA was more rapidly deadenylated as well as significantly stabilized in the ccr4∆ deadenylation mutant in the edc3∆ lsm4∆C background. These results suggest a role for these decapping factors in stabilizing mRNA and may implicate P bodies as sites of reduced mRNA degradation.
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80
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Shi W, Ma W, Xiong L, Zhang M, Tang C. Adaptation with transcriptional regulation. Sci Rep 2017; 7:42648. [PMID: 28233824 PMCID: PMC5324054 DOI: 10.1038/srep42648] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/10/2017] [Indexed: 11/21/2022] Open
Abstract
Biochemical adaptation is one of the basic functions that are widely implemented in biological systems for a variety of purposes such as signal sensing, stress response and homeostasis. The adaptation time scales span from milliseconds to days, involving different regulatory machineries in different processes. The adaptive networks with enzymatic regulation (ERNs) have been investigated in detail. But it remains unclear if and how other forms of regulation will impact the network topology and other features of the function. Here, we systematically studied three-node transcriptional regulatory networks (TRNs), with three different types of gene regulation logics. We found that the topologies of adaptive gene regulatory networks can still be grouped into two general classes: negative feedback loop (NFBL) and incoherent feed-forward loop (IFFL), but with some distinct topological features comparing to the enzymatic networks. Specifically, an auto-activation loop on the buffer node is necessary for the NFBL class. For IFFL class, the control node can be either a proportional node or an inversely-proportional node. Furthermore, the tunability of adaptive behavior differs between TRNs and ERNs. Our findings highlight the role of regulation forms in network topology, implementation and dynamics.
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Affiliation(s)
- Wenjia Shi
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Wenzhe Ma
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Liyang Xiong
- Center for Quantitative Biology, Peking University, Beijing 100871, China.,School of Physics, Peking University, Beijing 100871, China
| | - Mingyue Zhang
- Center for Quantitative Biology, Peking University, Beijing 100871, China.,School of Physics, Peking University, Beijing 100871, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing 100871, China.,School of Physics, Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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81
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Zhang R, Yuan H, Wang S, Ouyang Q, Chen Y, Hao N, Luo C. High-throughput single-cell analysis for the proteomic dynamics study of the yeast osmotic stress response. Sci Rep 2017; 7:42200. [PMID: 28181485 PMCID: PMC5299847 DOI: 10.1038/srep42200] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 01/06/2017] [Indexed: 11/22/2022] Open
Abstract
Motorized fluorescence microscopy combined with high-throughput microfluidic chips is a powerful method to obtain information about different biological processes in cell biology studies. Generally, to observe different strains under different environments, high-throughput microfluidic chips require complex preparatory work. In this study, we designed a novel and easily operated high-throughput microfluidic system to observe 96 different GFP-tagged yeast strains in one switchable culture condition or 24 different GFP-tagged yeast strains in four parallel switchable culture conditions. A multi-pipette is the only additional equipment required for high-throughput patterning of cells in the chip. Only eight connections are needed to control 96 conditions. Using these devices, the proteomic dynamics of the yeast stress response pathway were carefully studied based on single-cell data. A new method to characterize the proteomic dynamics using a single cell’s data is proposed and compared to previous methods, and the new technique should be useful for studying underlying control networks. Our method provides an easy and systematic way to study signaling pathways at the single-cell level.
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Affiliation(s)
- Rongfei Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Haiyu Yuan
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China
| | - Shujing Wang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Qi Ouyang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yong Chen
- Ecole Normale Superieure, 24 rue Lhomond, 75231 Paris, France
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Chunxiong Luo
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China
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82
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Klein M, Swinnen S, Thevelein JM, Nevoigt E. Glycerol metabolism and transport in yeast and fungi: established knowledge and ambiguities. Environ Microbiol 2017; 19:878-893. [DOI: 10.1111/1462-2920.13617] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/16/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Mathias Klein
- Department of Life Sciences and Chemistry; Jacobs University Bremen gGmbH; Campus Ring 1 Bremen 28759 Germany
| | - Steve Swinnen
- GlobalYeast NV; Kasteelpark Arenberg 31, Leuven-Heverlee 3001 Belgium
| | - Johan M. Thevelein
- GlobalYeast NV; Kasteelpark Arenberg 31, Leuven-Heverlee 3001 Belgium
- Laboratory of Molecular Cell Biology; Institute of Botany and Microbiology, KU Leuven; Leuven Belgium
- Department of Molecular Microbiology; VIB; Kasteelpark Arenberg 31, 3001 Heverlee-Leuven Flanders Belgium
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry; Jacobs University Bremen gGmbH; Campus Ring 1 Bremen 28759 Germany
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83
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Jogawat A, Vadassery J, Verma N, Oelmüller R, Dua M, Nevo E, Johri AK. PiHOG1, a stress regulator MAP kinase from the root endophyte fungus Piriformospora indica, confers salinity stress tolerance in rice plants. Sci Rep 2016; 6:36765. [PMID: 27849025 PMCID: PMC5111105 DOI: 10.1038/srep36765] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/20/2016] [Indexed: 12/04/2022] Open
Abstract
In this study, yeast HOG1 homologue from the root endophyte Piriformospora indica (PiHOG1) was isolated and functionally characterized. Functional expression of PiHOG1 in S. cerevisiae ∆hog1 mutant restored osmotolerance under high osmotic stress. Knockdown (KD) transformants of PiHOG1 generated by RNA interference in P. indica showed that genes for the HOG pathway, osmoresponse and salinity tolerance were less stimulated in KD-PiHOG1 compared to the wild-type under salinity stress. Furthermore, KD lines are impaired in the colonization of rice roots under salinity stress of 200 mM NaCl, and the biomass of the host plants, their shoot and root lengths, root number, photosynthetic pigment and proline contents were reduced as compared to rice plants colonized by WT P. indica. Therefore, PiHOG1 is critical for root colonisation, salinity tolerance and the performance of the host plant under salinity stress. Moreover, downregulation of PiHOG1 resulted not only in reduced and delayed phosphorylation of the remaining PiHOG1 protein in colonized salinity-stressed rice roots, but also in the downregulation of the upstream MAP kinase genes PiPBS2 and PiSSK2 involved in salinity tolerance signalling in the fungus. Our data demonstrate that PiHOG1 is not only involved in the salinity response of P. indica, but also helping host plant to overcome salinity stress.
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Affiliation(s)
- Abhimanyu Jogawat
- School of Life Sciences Jawaharlal Nehru University, New Delhi-110067, India
| | | | - Nidhi Verma
- School of Life Sciences Jawaharlal Nehru University, New Delhi-110067, India
| | - Ralf Oelmüller
- Institute of Plant Physiology, Friedrich-Schiller-University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Meenakshi Dua
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Eviatar Nevo
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, 199 Aba Khoushy Ave., Mount Carmel, Haifa, 3498838, Israel
| | - Atul Kumar Johri
- School of Life Sciences Jawaharlal Nehru University, New Delhi-110067, India
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84
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Lucas C, Ferreira C, Cazzanelli G, Franco-Duarte R, Tulha J, Roelink H, Conway SJ. Yeast Gup1(2) Proteins Are Homologues of the Hedgehog Morphogens Acyltransferases HHAT(L): Facts and Implications. J Dev Biol 2016; 4:E33. [PMID: 29615596 PMCID: PMC5831804 DOI: 10.3390/jdb4040033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 12/16/2022] Open
Abstract
In multiple tissues, the Hedgehog secreted morphogen activates in the receiving cells a pathway involved in cell fate, proliferation and differentiation in the receiving cells. This pathway is particularly important during embryogenesis. The protein HHAT (Hedgehog O-acyltransferase) modifies Hh morphogens prior to their secretion, while HHATL (Hh O-acyltransferase-like) negatively regulates the pathway. HHAT and HHATL are homologous to Saccharomyces cerevisiae Gup2 and Gup1, respectively. In yeast, Gup1 is associated with a high number and diversity of biological functions, namely polarity establishment, secretory/endocytic pathway functionality, vacuole morphology and wall and membrane composition, structure and maintenance. Phenotypes underlying death, morphogenesis and differentiation are also included. Paracrine signalling, like the one promoted by the Hh pathway, has not been shown to occur in microbial communities, despite the fact that large aggregates of cells like biofilms or colonies behave as proto-tissues. Instead, these have been suggested to sense the population density through the secretion of quorum-sensing chemicals. This review focuses on Gup1/HHATL and Gup2/HHAT proteins. We review the functions and physiology associated with these proteins in yeasts and higher eukaryotes. We suggest standardisation of the presently chaotic Gup-related nomenclature, which includes KIAA117, c3orf3, RASP, Skinny, Sightless and Central Missing, in order to avoid the disclosure of otherwise unnoticed information.
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Affiliation(s)
- Cândida Lucas
- CBMA—Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, 4710-054 Braga, Portugal; (G.C.); (R.F.-D.); (J.T.)
| | - Célia Ferreira
- CBMA—Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, 4710-054 Braga, Portugal; (G.C.); (R.F.-D.); (J.T.)
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK;
| | - Giulia Cazzanelli
- CBMA—Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, 4710-054 Braga, Portugal; (G.C.); (R.F.-D.); (J.T.)
| | - Ricardo Franco-Duarte
- CBMA—Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, 4710-054 Braga, Portugal; (G.C.); (R.F.-D.); (J.T.)
| | - Joana Tulha
- CBMA—Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, 4710-054 Braga, Portugal; (G.C.); (R.F.-D.); (J.T.)
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85
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Rodrigues LNDS, Brito WDA, Parente AFA, Weber SS, Bailão AM, Casaletti L, Borges CL, Soares CMDA. Osmotic stress adaptation of Paracoccidioides lutzii, Pb01, monitored by proteomics. Fungal Genet Biol 2016; 95:13-23. [DOI: 10.1016/j.fgb.2016.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 07/25/2016] [Accepted: 08/01/2016] [Indexed: 12/18/2022]
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86
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Hot1 factor recruits co-activator Sub1 and elongation complex Spt4/5 to osmostress genes. Biochem J 2016; 473:3065-79. [DOI: 10.1042/bcj20160463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/01/2016] [Indexed: 11/17/2022]
Abstract
Hyperosmotic stress response involves the adaptative mechanisms needed for cell survival. Under high osmolarity conditions, many stress response genes are activated by several unrelated transcription factors that are controlled by the Hog1 kinase. Osmostress transcription factor Hot1 regulates the expression of several genes involved in glycerol biosynthesis, and the presence of this transcription factor in their promoters is essential for RNApol II recruitment. The physical association between Hog1 and Hot1 activates this transcription factor and directs the RNA polymerase II localization at these promoters. We, herein, demonstrate that physical and genetic interactions exist between Hot1 and several proteins involved in transcriptional and posttranscriptional processes: for example, transcription co-activator Sub1 and elongation complex Spt4/5. The results presented in this work demonstrate that Hot1 enrichment is not detected through the coding regions of its target genes and rule out a direct role in transcription elongation. Instead, other data presented herein indicate a key function of the Hot1 transcription factor in the recruitment of these proteins to the promoter or the 5′-coding region of the genes under its control.
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87
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Tian L, Wang Y, Yu J, Xiong D, Zhao H, Tian C. The Mitogen-Activated Protein Kinase Kinase VdPbs2 of Verticillium dahliae Regulates Microsclerotia Formation, Stress Response, and Plant Infection. Front Microbiol 2016; 7:1532. [PMID: 27729908 PMCID: PMC5037172 DOI: 10.3389/fmicb.2016.01532] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/13/2016] [Indexed: 11/13/2022] Open
Abstract
Verticillium dahliae, a ubiquitous phytopathogenic fungus, forms resting structures, known as microsclerotia that play crucial roles in Verticillium wilt diseases. VdHog1, a mitogen-activated protein kinase (MAPK), controls microsclerotia formation, virulence, and stress response in V. dahliae. In this study, we present detailed evidence that the conserved upstream component of VdHog1, VdPbs2, is a key regulator of microsclerotia formation, oxidative stress and fungicide response and plant virulence in V. dahliae. We identified VdPbs2, homologous to the yeast MAPK kinase Pbs2. Similar to the VdHog1 deletion mutant, VdPbs2 deletion strains exhibited delayed melanin synthesis and reduced formation of microsclerotia. When exposed to stresses, VdPbs2 mutants were more sensitive than the wild type to osmotic agents and peroxide, but more resistant to inhibitors of cell wall synthesis and some fungicides. Finally, VdPbs2 deletion mutants exhibited reduced virulence on smoke tree and tobacco seedlings. When taken together, we implicate that VdPbs2 and VdHog1 function in a cascade that regulates microsclerotia formation and virulence, but not all VdHog1 dependent functions are VdPbs2 regulated. This study thus provides novel insights into the signal transduction mechanisms that regulate microsclerotia formation and pathogenesis in this fungus.
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Affiliation(s)
- Longyan Tian
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University Beijing, China
| | - Yonglin Wang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University Beijing, China
| | - Jun Yu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University Beijing, China
| | - Dianguang Xiong
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University Beijing, China
| | - Hengjun Zhao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University Beijing, China
| | - Chengming Tian
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University Beijing, China
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88
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Saxena A, Sitaraman R. Osmoregulation in Saccharomyces cerevisiae via mechanisms other than the high-osmolarity glycerol pathway. Microbiology (Reading) 2016; 162:1511-1526. [DOI: 10.1099/mic.0.000360] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Abhishek Saxena
- Department of Biotechnology, TERI University, New Delhi, India
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89
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Lu X, Wang Y, Zong H, Ji H, Zhuge B, Dong Z. Bioconversion of L-phenylalanine to 2-phenylethanol by the novel stress-tolerant yeast Candida glycerinogenes WL2002-5. Bioengineered 2016; 7:418-423. [PMID: 27435817 DOI: 10.1080/21655979.2016.1171437] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
2-Phenylethanol (2-PE) is a high value aromatic alcohol with a rose-like odor that is utilized in the cosmetics and other industries. Although the chemical routes of 2-PE production have been altered by some microbial transformation processes, the poor tolerance to organic solvents of these microorganisms has limited the 2-PE yield. In this study, the stress-tolerant yeast Candida glycerinogenes WL2002-5 showed a 2-PE tolerance to 4 g/l, which is the highest reported to date. Moreover, the 2-PE titer in a batch fermentation from L-phenylalanine reached 5g/l, which is the highest level achieved by fermentation without in situ product recovery. These results suggest C. glycerinogenes WL2002-5 is a robust strain for the bioproduction of 2-PE with potential for commercial exploitation.
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Affiliation(s)
- Xinyao Lu
- a The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China
| | - Yuqin Wang
- a The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China
| | - Hong Zong
- a The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China
| | - Hao Ji
- a The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China
| | - Bin Zhuge
- a The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China
| | - Zhuoli Dong
- b The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi , China
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90
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Genetic determinants for enhanced glycerol growth of Saccharomyces cerevisiae. Metab Eng 2016; 36:68-79. [DOI: 10.1016/j.ymben.2016.03.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/12/2016] [Accepted: 03/10/2016] [Indexed: 11/21/2022]
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91
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Ilyas S, Rehman A, Coelho AV, Sheehan D. Proteomic analysis of an environmental isolate of Rhodotorula mucilaginosa after arsenic and cadmium challenge: Identification of a protein expression signature for heavy metal exposure. J Proteomics 2016; 141:47-56. [DOI: 10.1016/j.jprot.2016.04.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 03/07/2016] [Accepted: 04/14/2016] [Indexed: 10/21/2022]
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92
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Hagiwara D, Sakamoto K, Abe K, Gomi K. Signaling pathways for stress responses and adaptation in Aspergillus species: stress biology in the post-genomic era. Biosci Biotechnol Biochem 2016; 80:1667-80. [PMID: 27007956 DOI: 10.1080/09168451.2016.1162085] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Aspergillus species are among the most important filamentous fungi in terms of industrial use and because of their pathogenic or toxin-producing features. The genomes of several Aspergillus species have become publicly available in this decade, and genomic analyses have contributed to an integrated understanding of fungal biology. Stress responses and adaptation mechanisms have been intensively investigated using the accessible genome infrastructure. Mitogen-activated protein kinase (MAPK) cascades have been highlighted as being fundamentally important in fungal adaptation to a wide range of stress conditions. Reverse genetics analyses have uncovered the roles of MAPK pathways in osmotic stress, cell wall stress, development, secondary metabolite production, and conidia stress resistance. This review summarizes the current knowledge on the stress biology of Aspergillus species, illuminating what we have learned from the genomic data in this "post-genomic era."
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Affiliation(s)
- Daisuke Hagiwara
- a Medical Mycology Research Center , Chiba University , Chiba , Japan
| | | | - Keietsu Abe
- c Graduate School of Agricultural Science , Tohoku University , Sendai , Japan
| | - Katsuya Gomi
- c Graduate School of Agricultural Science , Tohoku University , Sendai , Japan
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93
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Taymaz-Nikerel H, Cankorur-Cetinkaya A, Kirdar B. Genome-Wide Transcriptional Response of Saccharomyces cerevisiae to Stress-Induced Perturbations. Front Bioeng Biotechnol 2016; 4:17. [PMID: 26925399 PMCID: PMC4757645 DOI: 10.3389/fbioe.2016.00017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 02/04/2016] [Indexed: 12/22/2022] Open
Abstract
Cells respond to environmental and/or genetic perturbations in order to survive and proliferate. Characterization of the changes after various stimuli at different -omics levels is crucial to comprehend the adaptation of cells to the changing conditions. Genome-wide quantification and analysis of transcript levels, the genes affected by perturbations, extends our understanding of cellular metabolism by pointing out the mechanisms that play role in sensing the stress caused by those perturbations and related signaling pathways, and in this way guides us to achieve endeavors, such as rational engineering of cells or interpretation of disease mechanisms. Saccharomyces cerevisiae as a model system has been studied in response to different perturbations and corresponding transcriptional profiles were followed either statically or/and dynamically, short and long term. This review focuses on response of yeast cells to diverse stress inducing perturbations, including nutritional changes, ionic stress, salt stress, oxidative stress, osmotic shock, and to genetic interventions such as deletion and overexpression of genes. It is aimed to conclude on common regulatory phenomena that allow yeast to organize its transcriptomic response after any perturbation under different external conditions.
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Affiliation(s)
| | | | - Betul Kirdar
- Department of Chemical Engineering, Bogazici University , Istanbul , Turkey
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94
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de Lucena RM, Elsztein C, Barros de Souza R, de Barros Pita W, Paiva SDSL, de Morais MA. Genetic Interaction between HOG1 and SLT2 Genes in Signalling the Cellular Stress Caused by Sulphuric Acid in Saccharomyces cerevisiae. J Mol Microbiol Biotechnol 2016; 25:423-7. [PMID: 26845706 DOI: 10.1159/000443309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/09/2015] [Indexed: 11/19/2022] Open
Abstract
In fuel ethanol production, recycling of yeast biomass includes treatment of cells with diluted sulphuric acid in order to control bacterial population. However, this strategy might lead to a loss of cell viability, with potential negative consequences to the fermentation yield. In a recent paper we showed that the proteins Slt2 and Hog1 are essential for yeast tolerance to sulphuric acid. As a complement of the aforementioned work, we used DNA microarray technology to search for differentially expressed genes in hog1Δ and slt2Δ deletion mutants after treatment with sulphuric acid. Our results show how Slt2p and Hog1p could coordinate the interplay among protein kinase A (PKA), protein kinase C and high-osmolarity glycerol pathways. Moreover, the SSK22 and KDX1 genes may be part of this network, although their proteins were shown to be non-essential for cell growth/survival at low pH. These proteins might work by enhancing the signal which downregulates the PKA pathway leading to cell cycle arrest, in order to regenerate the integrity of yeast cell wall and cell homeostasis under acid shock.
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Affiliation(s)
- Rodrigo Mendonça de Lucena
- Interdepartmental Research Group in Metabolic Engineering, Federal University of Pernambuco, Recife, Brazil
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95
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A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae. PLoS Comput Biol 2016; 12:e1004703. [PMID: 26815455 PMCID: PMC4729481 DOI: 10.1371/journal.pcbi.1004703] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 12/13/2015] [Indexed: 11/20/2022] Open
Abstract
Cationic and heavy metal toxicity is involved in a substantial number of diseases in mammals and crop plants. Therefore, the understanding of tightly regulated transporter activities, as well as conceiving the interplay of regulatory mechanisms, is of substantial interest. A generalized thermodynamic description is developed for the complex interplay of the plasma membrane ion transporters, membrane potential and the consumption of energy for maintaining and restoring specific intracellular cation concentrations. This concept is applied to the homeostasis of cation concentrations in the yeast cells of S. cerevisiae. The thermodynamic approach allows to model passive ion fluxes driven by the electrochemical potential differences, but also primary or secondary active transport processes driven by the inter- play of different ions (symport, antiport) or by ATP consumption (ATPases). The model-confronted with experimental data-reproduces the experimentally observed potassium and proton fluxes induced by the external stimuli KCl and glucose. The estimated phenomenological constants combine kinetic parameters and transport coefficients. These are in good agreement with the biological understanding of the transporters thus providing a better understanding of the control exerted by the coupled fluxes. The model predicts the flux of additional ion species, like e.g. chloride, as a potential candidate for counterbalancing positive charges. Furthermore, the effect of a second KCl stimulus is simulated, predicting a reduced cellular response for cells that were first exposed to a high KCl stimulus compared to cells pretreated with a mild KCl stimulus. By describing the generalized forces that are responsible for a given flow, the model provides information and suggestions for new experiments. Furthermore, it can be extended to other systems such as e.g. Candida albicans, or selected plant cells.
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96
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Rose RE, Pazos MA, Curcio MJ, Fabris D. Global Epitranscriptomics Profiling of RNA Post-Transcriptional Modifications as an Effective Tool for Investigating the Epitranscriptomics of Stress Response. Mol Cell Proteomics 2016; 15:932-44. [PMID: 26733207 DOI: 10.1074/mcp.m115.054718] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Indexed: 02/01/2023] Open
Abstract
The simultaneous detection of all the post-transcriptional modifications (PTMs) that decorate cellular RNA can provide comprehensive information on the effects of changing environmental conditions on the entire epitranscriptome. To capture this type of information, we performed the analysis of ribonucleotide mixtures produced by hydrolysis of total RNA extracts from S. cerevisiae that was grown under hyperosmotic and heat shock conditions. Their global PTM profiles clearly indicated that the cellular responses to these types of stresses involved profound changes in the production of specific PTMs. The observed changes involved not only up-/down-regulation of typical PTMs, but also the outright induction of new ones that were absent under normal conditions, or the elimination of others that were normally present. Pointing toward the broad involvement of different classes of RNAs, many of the newly observed PTMs differed from those engaged in the known tRNA-based mechanism of translational recoding, which is induced by oxidative stress. Some of the expression effects were stress-specific, whereas others were not, thus suggesting that RNA PTMs may perform multifaceted activities in stress response, which are subjected to distinctive regulatory pathways. To explore their signaling networks, we implemented a strategy based on the systematic deletion of genes that connect established response genes with PTM biogenetic enzymes in a putative interactomic map. The results clearly identified PTMs that were under direct HOG control, a well-known protein kinase pathway involved in stress response in eukaryotes. Activation of this signaling pathway has been shown to result in the stabilization of numerous mRNAs and the induction of selected lncRNAs involved in chromatin remodeling. The fact that PTMs are capable of altering the activity of the parent RNAs suggest their possible participation in feedback mechanisms aimed at modulating the regulatory functions of such RNAs. This tantalizing hypothesis will be the object of future studies.
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Affiliation(s)
- Rebecca E Rose
- From the ‡The RNA Institute, University at Albany (SUNY), Albany, New York 12222
| | - Manuel A Pazos
- From the ‡The RNA Institute, University at Albany (SUNY), Albany, New York 12222
| | - M Joan Curcio
- From the ‡The RNA Institute, University at Albany (SUNY), Albany, New York 12222; ‖Laboratory of Molecular Genetics, Wadsworth Center, Albany, New York 12208
| | - Daniele Fabris
- From the ‡The RNA Institute, University at Albany (SUNY), Albany, New York 12222;
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97
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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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98
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Sharifian H, Lampert F, Stojanovski K, Regot S, Vaga S, Buser R, Lee SS, Koeppl H, Posas F, Pelet S, Peter M. Parallel feedback loops control the basal activity of the HOG MAPK signaling cascade. Integr Biol (Camb) 2015; 7:412-22. [PMID: 25734609 DOI: 10.1039/c4ib00299g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Tight regulation of the MAP kinase Hog1 is crucial for survival under changing osmotic conditions. Interestingly, we found that Hog1 phosphorylates multiple upstream components, implying feedback regulation within the signaling cascade. Taking advantage of an unexpected link between glucose availability and Hog1 activity, we used quantitative single cell measurements and computational modeling to unravel feedback regulation operating in addition to the well-known adaptation feedback triggered by glycerol accumulation. Indeed, we found that Hog1 phosphorylates its activating kinase Ssk2 on several sites, and cells expressing a non-phosphorylatable Ssk2 mutant are partially defective for feedback regulation and proper control of basal Hog1 activity. Together, our data suggest that Hog1 activity is controlled by intertwined regulatory mechanisms operating with varying kinetics, which together tune the Hog1 response to balance basal Hog1 activity and its steady-state level after adaptation to high osmolarity.
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Affiliation(s)
- Hoda Sharifian
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland.
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99
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Teixeira V, Costa V. Unraveling the role of the Target of Rapamycin signaling in sphingolipid metabolism. Prog Lipid Res 2015; 61:109-33. [PMID: 26703187 DOI: 10.1016/j.plipres.2015.11.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 11/04/2015] [Accepted: 11/09/2015] [Indexed: 02/06/2023]
Abstract
Sphingolipids are important bioactive molecules that regulate basic aspects of cellular metabolism and physiology, including cell growth, adhesion, migration, senescence, apoptosis, endocytosis, and autophagy in yeast and higher eukaryotes. Since they have the ability to modulate the activation of several proteins and signaling pathways, variations in the relative levels of different sphingolipid species result in important changes in overall cellular functions and fate. Sphingolipid metabolism and their route of synthesis are highly conserved from yeast to mammalian cells. Studies using the budding yeast Saccharomyces cerevisiae have served in many ways to foster our understanding of sphingolipid dynamics and their role in the regulation of cellular processes. In the past decade, studies in S. cerevisiae have unraveled a functional association between the Target of Rapamycin (TOR) pathway and sphingolipids, showing that both TOR Complex 1 (TORC1) and TOR Complex 2 (TORC2) branches control temporal and spatial aspects of sphingolipid metabolism in response to physiological and environmental cues. In this review, we report recent findings in this emerging and exciting link between the TOR pathway and sphingolipids and implications in human health and disease.
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Affiliation(s)
- Vitor Teixeira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; IBMC, Instituto de Biologia Molecular e Celular, Porto, Portugal; ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Departamento de Biologia Molecular, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Vítor Costa
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; IBMC, Instituto de Biologia Molecular e Celular, Porto, Portugal; ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Departamento de Biologia Molecular, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
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100
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Noti O, Vaudano E, Pessione E, Garcia-Moruno E. Short-term response of different Saccharomyces cerevisiae strains to hyperosmotic stress caused by inoculation in grape must: RT-qPCR study and metabolite analysis. Food Microbiol 2015; 52:49-58. [DOI: 10.1016/j.fm.2015.06.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 06/26/2015] [Accepted: 06/29/2015] [Indexed: 10/23/2022]
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