101
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Ethanol induces calcium influx via the Cch1-Mid1 transporter in Saccharomyces cerevisiae. Arch Microbiol 2011; 193:323-34. [PMID: 21259000 DOI: 10.1007/s00203-010-0673-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 12/02/2010] [Accepted: 12/24/2010] [Indexed: 10/18/2022]
Abstract
Yeast suffers from a variety of environmental stresses, such as osmotic pressure and ethanol produced during fermentation. Since calcium ions are protective for high concentrations of ethanol, we investigated whether Ca(2+) flux occurs in response to ethanol stress. We find that exposure of yeast to ethanol induces a rise in the cytoplasmic concentration of Ca(2+). The response is enhanced in cells shifted to high-osmotic media containing proline, galactose, sorbitol, or mannitol. Suspension of cells in proline and galactose-containing media increases the Ca(2+) levels in the cytoplasm independent of ethanol exposure. The enhanced ability for ethanol to induce Ca(2+) flux after the hypertonic shift is transient, decreasing rapidly over a period of seconds to minutes. There is partial recovery of the response after zymolyase treatment, suggesting that cell wall integrity affects the ethanol-induced Ca(2+) flux. Acetate inhibits the Ca(2+) accumulation elicited by the ethanol/osmotic stress. The Ca(2+) flux is primarily via the Cch1 Ca(2+) influx channel because strains carrying deletions of the cch1 and mid1 genes show greater than 90% reduction in Ca(2+) flux. Furthermore, a functional Cch1 channel reduced growth inhibition by ethanol.
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102
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Dragosits M, Mattanovich D, Gasser B. Induction and measurement of UPR and osmotic stress in the yeast Pichia pastoris. Methods Enzymol 2011; 489:165-88. [PMID: 21266230 DOI: 10.1016/b978-0-12-385116-1.00010-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Unfolded protein response (UPR) is a major reaction to intrinsic stress of eukaryotic organisms and is also related to environmental stress reactions. Among yeasts, stress regulation has mainly been investigated in Saccharomyces cerevisiae, while other species with biotechnological or medical interest are less well understood. Pichia pastoris as one example has emerged as a favorite production platform for recombinant proteins during the last two decades. UPR and environmental stress are well known to interfere with the production of recombinant proteins as well as other technologically relevant processes, so that the demand for well-documented protocols to measure such stress reactions has strongly increased. Here, we describe protocols for the induction of UPR and osmotic stress, as well as for the quantitative measurement of cellular stress reactions at the levels of transcripts, proteins, and metabolites. As such protocols need to be adapted for a new species of interest, the guidelines presented here should enable researchers to study P. pastoris directly without the hassle to modify standard protocols designed for the model organism S. cerevisiae first.
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Affiliation(s)
- Martin Dragosits
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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103
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Pang K, Cheng C, Xuan Z, Sheng H, Ma X. Understanding protein evolutionary rate by integrating gene co-expression with protein interactions. BMC SYSTEMS BIOLOGY 2010; 4:179. [PMID: 21190591 PMCID: PMC3022652 DOI: 10.1186/1752-0509-4-179] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 12/30/2010] [Indexed: 12/23/2022]
Abstract
Background Among the many factors determining protein evolutionary rate, protein-protein interaction degree (PPID) has been intensively investigated in recent years, but its precise effect on protein evolutionary rate is still heavily debated. Results We first confirmed that the correlation between protein evolutionary rate and PPID varies considerably across different protein interaction datasets. Specifically, because of the maximal inconsistency between yeast two-hybrid and other datasets, we reasoned that the difference in experimental methods contributes to our inability to clearly define how PPID affects protein evolutionary rate. To address this, we integrated protein interaction and gene co-expression data to derive a co-expressed protein-protein interaction degree (ePPID) measure, which reflects the number of partners with which a protein can permanently interact. Thus, irrespective of the experimental method employed, we found that (1) ePPID is a better predictor of protein evolutionary rate than PPID, (2) ePPID is a more robust predictor of protein evolutionary rate than PPID, and (3) the contribution of ePPID to protein evolutionary rate is statistically independent of expression level. Analysis of hub proteins in the Structural Interaction Network further supported ePPID as a better predictor of protein evolutionary rate than the number of distinct binding interfaces and clarified the slower evolution of co-expressed multi-interface hub proteins over that of other hub proteins. Conclusions Our study firmly established ePPID as a robust predictor of protein evolutionary rate, irrespective of experimental method, and underscored the importance of permanent interactions in shaping the evolutionary outcome.
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Affiliation(s)
- Kaifang Pang
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, China
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104
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Rodríguez-Peña JM, García R, Nombela C, Arroyo J. The high-osmolarity glycerol (HOG) and cell wall integrity (CWI) signalling pathways interplay: a yeast dialogue between MAPK routes. Yeast 2010; 27:495-502. [PMID: 20641030 DOI: 10.1002/yea.1792] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Two mitogen-activated protein kinase (MAPK) pathways, viz. the high-osmolarity glycerol (HOG) and the cell wall integrity (CWI) pathways, regulate stress responses in the yeast Saccharomyces cerevisiae. Whereas the former is mainly involved in adaptation of yeast cells to hyperosmotic stress, the latter is activated under conditions leading to cell wall instability. Although MAPK signalling specificity can be conceived as requiring insulation of the different pathways, it is also becoming clear that the two pathways do not compete with each other but can be positively coordinated to regulate many stress responses. This review highlights our current knowledge about the collaboration between these two MAPK pathways to counteract different kinds of environmental stress.
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Affiliation(s)
- Jose Manuel Rodríguez-Peña
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid (UCM), IRYCIS, 28040 Madrid, Spain
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105
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Qian J, Qin X, Yin Q, Chu J, Wang Y. Cloning and characterization of Kluyveromyces marxianus Hog1 gene. Biotechnol Lett 2010; 33:571-5. [DOI: 10.1007/s10529-010-0458-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 10/22/2010] [Indexed: 11/28/2022]
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106
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Patterson JC, Klimenko ES, Thorner J. Single-cell analysis reveals that insulation maintains signaling specificity between two yeast MAPK pathways with common components. Sci Signal 2010; 3:ra75. [PMID: 20959523 DOI: 10.1126/scisignal.2001275] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Eukaryotic cells use multiple mitogen-activated protein kinase (MAPK) cascades to evoke appropriate responses to external stimuli. In Saccharomyces cerevisiae, the MAPK Fus3 is activated by pheromone-binding heterotrimeric guanosine triphosphate-binding protein (G protein)-coupled receptors to promote mating, whereas the MAPK Hog1 is activated by hyperosmotic stress to elicit the high-osmolarity glycerol (HOG) response. Although these MAPK pathways share several upstream components, exposure to either pheromone or osmolyte alone triggers only the appropriate response. We used fluorescence localization- and transcription-specific reporters to assess activation of these pathways in individual cells on the minute and hour time scale, respectively. Dual activation of these two MAPK pathways occurred over a broad range of stimulant concentrations and temporal regimes in wild-type cells subjected to costimulation. Thus, signaling specificity is achieved through an "insulation" mechanism, not a "cross-inhibition" mechanism. Furthermore, we showed that there was a critical period during which Hog1 activity had to occur for proper insulation of the HOG pathway.
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Affiliation(s)
- Jesse C Patterson
- Division of Biochemistry and Molecular Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA
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107
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Pang K, Sheng H, Ma X. Understanding gene essentiality by finely characterizing hubs in the yeast protein interaction network. Biochem Biophys Res Commun 2010; 401:112-6. [PMID: 20833129 DOI: 10.1016/j.bbrc.2010.09.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Accepted: 09/05/2010] [Indexed: 10/19/2022]
Abstract
The centrality-lethality rule, i.e., high-degree proteins or hubs tend to be more essential than low-degree proteins in the yeast protein interaction network, reveals that a protein's central position indicates its important function, but whether and why hubs tend to be more essential have been heavily debated. Here, we integrated gene expression and functional module data to classify hubs into four types: non-co-expressed non-co-cluster hubs, non-co-expressed co-cluster hubs, co-expressed non-co-cluster hubs and co-expressed co-cluster hubs. We found that all the four hub types are more essential than non-hubs, but they also show different enrichments in essential proteins. Non-co-expressed non-co-cluster hubs play key role in organizing different modules formed by the other three hub types, but they are less important to the survival of the yeast cell. Among the four hub types, co-expressed co-cluster hubs, which likely correspond to the core components of stable protein complexes, are the most essential. These results demonstrated that our classification of hubs into four types could better improve the understanding of gene essentiality.
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Affiliation(s)
- Kaifang Pang
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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108
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Activation of the heat shock transcription factor Hsf1 is essential for the full virulence of the fungal pathogen Candida albicans. Fungal Genet Biol 2010; 48:297-305. [PMID: 20817114 PMCID: PMC3032048 DOI: 10.1016/j.fgb.2010.08.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Revised: 08/23/2010] [Accepted: 08/23/2010] [Indexed: 01/09/2023]
Abstract
The evolutionarily conserved heat shock transcription factor Hsf1 plays a central role in thermal adaptation in the major fungal pathogen of humans, Candida albicans. Hsf1 becomes hyperphosphorylated in response to heat shock and activates the transcription of genes with heat shock elements (HSEs) in their promoters, these genes contributing to thermal adaptation. However, the relevance of Hsf1 activation to C. albicans virulence is not clear as this pathogen is thought to be obligately associated with warm blooded animals, and this issue has not been tested because HSF1 is essential for viability in C. albicans. In this study, we demonstrate that the HSE regulon is active in C. albicans cells infecting the kidney. We also show the CE2 region of Hsf1 is required for activation and that the phosphorylation of specific residues in this domain contributes to Hsf1 activation. C. albicans HSF1 mutants that lack this CE2 region are viable. However, they are unable to activate HSE-containing genes in response to heat shock, and they are thermosensitive. Using this HSF1 CE2 deletion mutant we demonstrate that Hsf1 activation, and hence thermal adaptation, contributes significantly to the virulence of C. albicans.
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109
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Wu X, Chi X, Wang P, Zheng D, Ding R, Li Y. The evolutionary rate variation among genes of HOG-signaling pathway in yeast genomes. Biol Direct 2010; 5:46. [PMID: 20618989 PMCID: PMC2914728 DOI: 10.1186/1745-6150-5-46] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Accepted: 07/10/2010] [Indexed: 11/10/2022] Open
Abstract
Background Responses to extracellular stress are required for microbes to survive in changing environments. Although the stress response mechanisms have been characterized extensively, the evolution of stress response pathway remains poorly understood. Here, we studied the evolution of High Osmolarity Glycerol (HOG) pathway, one of the important osmotic stress response pathways, across 10 yeast species and underpinned the evolutionary forces acting on the pathway evolution. Results Although the HOG pathway is well conserved across the surveyed yeast species, the evolutionary rate of the genes in this pathway varied substantially among or within different lineages. The fast divergence of MSB2 gene indicates that this gene is subjected to positive selection. Moreover, transcription factors in HOG pathway tend to evolve more rapidly, but the genes in conserved MAPK cascade underwent stronger functional selection. Remarkably, the dN/dS values are negatively correlated with pathway position along HOG pathway from Sln1 (Sho1) to Hog1 for transmitting external signal into nuclear. The increased gradient of selective constraints from upstream to downstream genes suggested that the downstream genes are more pleiotropic, being required for a wider range of pathways. In addition, protein length, codon usage, gene expression, and protein interaction appear to be important factors to determine the evolution of genes in HOG pathway. Conclusions Taken together, our results suggest that functional constraints play a large role in the evolutionary rate variation in HOG pathway, but the genetic variation was influenced by quite complicated factors, such as pathway position, protein length and so on. These findings provide some insights into how HOG pathway genes evolved rapidly for responding to environmental osmotic stress changes. Reviewers This article was reviewed by Han Liang (nominated by Laura Landweber), Georgy Bazykin (nominated by Mikhail Gelfand) and Zhenguo Lin (nominated by John Logsdon).
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Affiliation(s)
- Xuechang Wu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, PR China.
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110
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Correia I, Alonso-Monge R, Pla J. MAPK cell-cycle regulation in Saccharomyces cerevisiae and Candida albicans. Future Microbiol 2010; 5:1125-41. [DOI: 10.2217/fmb.10.72] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The cell cycle is the sequential set of events that living cells undergo in order to duplicate. This process must be tightly regulated as alterations may lead to diseases such as cancer. The molecular events that control the cell cycle are directional and involve regulatory molecules such as cyclins and cyclin-dependent kinases (CDKs). The budding yeast Saccharomyces cerevisiae has become a model to study this complex system since it shares several mechanisms with higher eukaryotes. Signal transduction pathways are biochemical mechanisms that sense environmental changes and there is recent evidence that they control the progression through the cell cycle in response to several stimuli. In response to pheromone, the budding yeast arrests the cell cycle in the G1 phase at the START stage. Activation of the pheromone response pathway leads to the phosphorylation of Far1, which inhibits the function of complexes formed by G1 cyclins (Cln1 and Cln2) and the CDK (Cdc28), blocking the transition to the S phase. This response prepares the cells to fuse cytoplasms and nuclei to generate a diploid cell. Activation of the Hog1 MAP kinase in response to osmotic stress or arsenite leads to the transient arrest of the cell cycle in G1 phase, which is mediated by direct phosphorylation of the CDK inhibitor, Sic1, and by downregulation of cyclin expression. Osmotic stress also induces a delay in G2 phase by direct phosphorylation of Hsl7 via Hog1, which results in the accumulation of Swe1. As a consequence, cell cycle arrest allows cells to survive upon stress. Finally, cell wall damage can induce cell cycle arrest at G2 via the cell integrity MAPK Slt2. By linking MAPK signal transduction pathways to the cell cycle machinery, a tight and precise control of the cell division takes place in response to environmental changes. Research into similar MAPK-mediated cell cycle regulation in the opportunistic pathogen Candida albicans may result in the development of new antifungal therapies.
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Affiliation(s)
- Inês Correia
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, E-28040 Madrid, Spain
| | - Rebeca Alonso-Monge
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, E-28040 Madrid, Spain
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111
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Torres-Quiroz F, García-Marqués S, Coria R, Randez-Gil F, Prieto JA. The activity of yeast Hog1 MAPK is required during endoplasmic reticulum stress induced by tunicamycin exposure. J Biol Chem 2010; 285:20088-96. [PMID: 20430884 DOI: 10.1074/jbc.m109.063578] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Accumulation of unfolded proteins in the endoplasmic reticulum (ER) triggers the so-called unfolded protein response (UPR), a conserved signaling pathway that drives the transcription of genes such as chaperones and folding enzymes. Nevertheless, the activity of the UPR accounts only for a part of the gene expression program activated upon ER stress. Moreover, the mechanism(s) for how cells adapt and survive to this stress are largely unknown. Here, we show that the yeast high osmolarity glycerol (HOG) pathway plays a role in ER stress resistance. Strains lacking the MAPK Hog1p displayed sensitivity to tunicamycin or beta-mercaptoethanol, whereas hyperactivation of the pathway enhanced their resistance. However, these effects were not due to Hog1p-mediated regulation of the UPR. Northern blot analysis demonstrated that Hog1p controls the tunicamycin-induced transcriptional change of GPD1 and that wild-type cells exposed to the drug accumulated glycerol in a Hog1p-dependent manner. Consistent with this, deletion of genes involved in glycerol synthesis caused increased sensitivity to tunicamycin, whereas overexpression of GPD1 provided higher tolerance to both wild-type and hog1Delta mutant cells. Quite remarkably, these effects were mediated by the basal activity of the MAPK because tunicamycin exposure does not trigger the phosphorylation of Hog1p or its nuclear import. Hence, our results describe new aspects of the yeast response to ER stress and identify additional functions of glycerol and the Hog1p MAPK to provide stress resistance.
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Affiliation(s)
- Francisco Torres-Quiroz
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, E-46100 Burjassot, Valencia, Spain
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112
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Bicknell AA, Tourtellotte J, Niwa M. Late phase of the endoplasmic reticulum stress response pathway is regulated by Hog1 MAP kinase. J Biol Chem 2010; 285:17545-55. [PMID: 20382742 DOI: 10.1074/jbc.m109.084681] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
When unfolded proteins accumulate in the endoplasmic reticulum (ER) causing ER stress, the unfolded protein response (UPR) responds rapidly to induce a transcriptional program that functions to alleviate the stress. However, under extreme conditions, when UPR activation is not sufficient to alleviate ER stress, the stress may persist long term. Very little is known about how the cell responds to persistent ER stress that is not resolved by the immediate activation of the UPR. We show that Hog1 MAP kinase becomes phosphorylated during the late stage of ER stress and helps the ER regain homeostasis. Although Hog1 is well known to function in osmotic stress and cell wall integrity pathways, we show that the activation mechanism for Hog1 during ER stress is distinct from both of these pathways. During late stage ER stress, upon phosphorylation, Hog1 translocates into the nucleus and regulates gene expression. Subsequently, Hog1 returns to the cytoplasm, where its phosphorylation levels remain high. From its cytoplasmic location, Hog1 contributes to the activation of autophagy by enhancing the stability of Atg8, a critical autophagy protein. Thus, Hog1 coordinates a multifaceted response to persistent ER stress.
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Affiliation(s)
- Alicia A Bicknell
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, USA
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113
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Dragosits M, Stadlmann J, Graf A, Gasser B, Maurer M, Sauer M, Kreil DP, Altmann F, Mattanovich D. The response to unfolded protein is involved in osmotolerance of Pichia pastoris. BMC Genomics 2010; 11:207. [PMID: 20346137 PMCID: PMC2867824 DOI: 10.1186/1471-2164-11-207] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 03/26/2010] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The effect of osmolarity on cellular physiology has been subject of investigation in many different species. High osmolarity is of importance for biotechnological production processes, where high cell densities and product titers are aspired. Several studies indicated that increased osmolarity of the growth medium can have a beneficial effect on recombinant protein production in different host organisms. Thus, the effect of osmolarity on the cellular physiology of Pichia pastoris, a prominent host for recombinant protein production, was studied in carbon limited chemostat cultures at different osmolarities. Transcriptome and proteome analyses were applied to assess differences upon growth at different osmolarities in both, a wild type strain and an antibody fragment expressing strain. While our main intention was to analyze the effect of different osmolarities on P. pastoris in general, this was complemented by studying it in context with recombinant protein production. RESULTS In contrast to the model yeast Saccharomyces cerevisiae, the main osmolyte in P. pastoris was arabitol rather than glycerol, demonstrating differences in osmotic stress response as well as energy metabolism. 2D Fluorescence Difference Gel electrophoresis and microarray analysis were applied and demonstrated that processes such as protein folding, ribosome biogenesis and cell wall organization were affected by increased osmolarity. These data indicated that upon increased osmolarity less adaptations on both the transcript and protein level occurred in a P. pastoris strain, secreting the Fab fragment, compared with the wild type strain. No transcriptional activation of the high osmolarity glycerol (HOG) pathway was observed at steady state conditions. Furthermore, no change of the specific productivity of recombinant Fab was observed at increased osmolarity. CONCLUSION These data point out that the physiological response to increased osmolarity is different to S. cerevisiae. Increased osmolarity resulted in an unfolded protein response (UPR) like response in P. pastoris and lead to pre-conditioning of the recombinant Fab producing strain of P. pastoris to growth at high osmolarity. The current data demonstrate a strong similarity of environmental stress response mechanisms and recombinant protein related stresses. Therefore, these results might be used in future strain and bioprocess engineering of this biotechnologically relevant yeast.
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Affiliation(s)
- Martin Dragosits
- Department of Biotechnology, BOKU-University of Natural Resources and Applied Life Sciences, Vienna, Austria
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114
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Chavel CA, Dionne HM, Birkaya B, Joshi J, Cullen PJ. Multiple signals converge on a differentiation MAPK pathway. PLoS Genet 2010; 6:e1000883. [PMID: 20333241 PMCID: PMC2841618 DOI: 10.1371/journal.pgen.1000883] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Accepted: 02/14/2010] [Indexed: 12/12/2022] Open
Abstract
An important emerging question in the area of signal transduction is how information from different pathways becomes integrated into a highly coordinated response. In budding yeast, multiple pathways regulate filamentous growth, a complex differentiation response that occurs under specific environmental conditions. To identify new aspects of filamentous growth regulation, we used a novel screening approach (called secretion profiling) that measures release of the extracellular domain of Msb2p, the signaling mucin which functions at the head of the filamentous growth (FG) MAPK pathway. Secretion profiling of complementary genomic collections showed that many of the pathways that regulate filamentous growth (RAS, RIM101, OPI1, and RTG) were also required for FG pathway activation. This regulation sensitized the FG pathway to multiple stimuli and synchronized it to the global signaling network. Several of the regulators were required for MSB2 expression, which identifies the MSB2 promoter as a target “hub” where multiple signals converge. Accessibility to the MSB2 promoter was further regulated by the histone deacetylase (HDAC) Rpd3p(L), which positively regulated FG pathway activity and filamentous growth. Our findings provide the first glimpse of a global regulatory hierarchy among the pathways that control filamentous growth. Systems-level integration of signaling circuitry is likely to coordinate other regulatory networks that control complex behaviors. Signal integration is an essential feature of information flow through signal transduction pathways. The mechanisms by which signals from multiple pathways become integrated into a coordinated response remain unclear. We show that multiple pathways that regulate filamentous growth converge on a differentiation-dependent MAPK pathway. Our findings indicate that more extensive communication occurs between signaling pathways that control the filamentation response than has previously been appreciated. We suggest that global communication hierarchies regulate information flow in other systems, particularly higher eukaryotes where multiple pathways typically function simultaneously to modulate a complex response.
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Affiliation(s)
- Colin A. Chavel
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Heather M. Dionne
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Barbara Birkaya
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Jyoti Joshi
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Paul J. Cullen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
- * E-mail:
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115
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Parkkinen JA, Kaski S. Searching for functional gene modules with interaction component models. BMC SYSTEMS BIOLOGY 2010; 4:4. [PMID: 20100324 PMCID: PMC2823677 DOI: 10.1186/1752-0509-4-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Accepted: 01/25/2010] [Indexed: 12/04/2022]
Abstract
BACKGROUND Functional gene modules and protein complexes are being sought from combinations of gene expression and protein-protein interaction data with various clustering-type methods. Central features missing from most of these methods are handling of uncertainty in both protein interaction and gene expression measurements, and in particular capability of modeling overlapping clusters. It would make sense to assume that proteins may play different roles in different functional modules, and the roles are evidenced in their interactions. RESULTS We formulate a generative probabilistic model for protein-protein interaction links and introduce two ways for including gene expression data into the model. The model finds interaction components, which can be interpreted as overlapping clusters or functional modules. We demonstrate the performance on two data sets of yeast Saccharomyces cerevisiae. Our methods outperform a representative set of earlier models in the task of finding biologically relevant modules having enriched functional classes. CONCLUSIONS Combining protein interaction and gene expression data with a probabilistic generative model improves discovery of modules compared to approaches based on either data source alone. With a fairly simple model we can find biologically relevant modules better than with alternative methods, and in addition the modules may be inherently overlapping in the sense that different interactions may belong to different modules.
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Affiliation(s)
- Juuso A Parkkinen
- Helsinki Institute for Information Technology HIIT and Adaptive Informatics Research Centre, Department of Information and Computer Science, Helsinki University of Technology, P.O. Box 5400, FI-02015 TKK, Finland
- Department of Computer Science, P.O. Box 68, FI-00014, University of Helsinki, Finland
| | - Samuel Kaski
- Helsinki Institute for Information Technology HIIT and Adaptive Informatics Research Centre, Department of Information and Computer Science, Helsinki University of Technology, P.O. Box 5400, FI-02015 TKK, Finland
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116
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Hohmann S. Control of high osmolarity signalling in the yeast Saccharomyces cerevisiae. FEBS Lett 2010; 583:4025-9. [PMID: 19878680 DOI: 10.1016/j.febslet.2009.10.069] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Accepted: 10/26/2009] [Indexed: 12/01/2022]
Abstract
Signal transduction pathways control cellular responses to extrinsic and intrinsic signals. The yeast HOG (High Osmolarity Glycerol) response pathway mediates cellular adaptation to hyperosmotic stress. Pathway architecture as well as the flow of signal have been studied to a very high degree of detail. Recently, the yeast HOG pathway has become a popular model to analyse systems level properties of signal transduction. Those studies addressed, using experimentation and modelling, the role of basal signalling, robustness against perturbation, as well as adaptation and feedback control. These recent findings provide exciting insight into the higher control levels of signalling through this MAPK system of potential general importance.
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Affiliation(s)
- Stefan Hohmann
- Department of Cell and Molecular Biology, University of Gothenburg, Göteborg, Sweden.
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117
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Ulitsky I, Krogan NJ, Shamir R. Towards accurate imputation of quantitative genetic interactions. Genome Biol 2009; 10:R140. [PMID: 20003301 PMCID: PMC2812947 DOI: 10.1186/gb-2009-10-12-r140] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Revised: 11/08/2009] [Accepted: 12/10/2009] [Indexed: 12/25/2022] Open
Abstract
A new method for calculating quantitative genetic interactions allows for the inference of 190,000 new genetic interactions in Saccharomyces cerevisae. Recent technological breakthroughs have enabled high-throughput quantitative measurements of hundreds of thousands of genetic interactions among hundreds of genes in Saccharomyces cerevisiae. However, these assays often fail to measure the genetic interactions among up to 40% of the studied gene pairs. Here we present a novel method, which combines genetic interaction data together with diverse genomic data, to quantitatively impute these missing interactions. We also present data on almost 190,000 novel interactions.
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Affiliation(s)
- Igor Ulitsky
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.
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118
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Multilayered control of gene expression by stress-activated protein kinases. EMBO J 2009; 29:4-13. [PMID: 19942851 DOI: 10.1038/emboj.2009.346] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Accepted: 11/02/2009] [Indexed: 11/09/2022] Open
Abstract
Stress-activated protein kinases (SAPKs) are key elements for intracellular signalling networks that serve to respond and adapt to extracellular changes. Exposure of yeast to high osmolarity results in the activation of p38-related SAPK, Hog1, which is essential for reprogramming the gene expression capacity of the cell by regulation of several steps of the transcription process. At initiation, active Hog1 not only directly phosphorylates several transcription factors to alter their activities, but also associates at stress-responsive promoters through such transcription factors. Once at the promoters, Hog1 serves as a platform to recruit general transcription factors, chromatin-modifying activities and RNA Pol II. In addition, the SAPK pathway has a role in elongation. At the stress-responsive ORFs, Hog1 recruits the RSC chromatin-remodelling complex to modify nucleosome organization. Several SAPKs from yeast to mammals have maintained some of the regulatory abilities of Hog1. Thus, elucidating the control of gene expression by the Hog1 SAPK should help to understand how eukaryotic cells implement a massive and rapid change on their transcriptional capacity in response to adverse conditions.
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119
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Muzzey D, Gómez-Uribe CA, Mettetal JT, van Oudenaarden A. A systems-level analysis of perfect adaptation in yeast osmoregulation. Cell 2009; 138:160-71. [PMID: 19596242 DOI: 10.1016/j.cell.2009.04.047] [Citation(s) in RCA: 238] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2008] [Revised: 01/22/2009] [Accepted: 04/13/2009] [Indexed: 11/16/2022]
Abstract
Negative feedback can serve many different cellular functions, including noise reduction in transcriptional networks and the creation of circadian oscillations. However, only one special type of negative feedback ("integral feedback") ensures perfect adaptation, where steady-state output is independent of steady-state input. Here we quantitatively measure single-cell dynamics in the Saccharomyces cerevisiae hyperosmotic shock network, which regulates membrane turgor pressure. Importantly, we find that the nuclear enrichment of the MAP kinase Hog1 perfectly adapts to changes in external osmolarity, a feature robust to signaling fidelity and operating with very low noise. By monitoring multiple system quantities (e.g., cell volume, Hog1, glycerol) and using varied input waveforms (e.g., steps and ramps), we assess in a minimally invasive manner the network location of the mechanism responsible for perfect adaptation. We conclude that the system contains only one effective integrating mechanism, which requires Hog1 kinase activity and regulates glycerol synthesis but not leakage.
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Affiliation(s)
- Dale Muzzey
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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120
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Mollapour M, Shepherd A, Piper PW. Presence of the Fps1p aquaglyceroporin channel is essential for Hog1p activation, but suppresses Slt2(Mpk1)p activation, with acetic acid stress of yeast. MICROBIOLOGY-SGM 2009; 155:3304-3311. [PMID: 19608606 DOI: 10.1099/mic.0.030502-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
When grown at pH 4.5, Saccharomyces cerevisiae acquires a resistance to inhibitory acetic acid levels ( approximately 0.1 M) by destabilizing Fps1p, the plasma membrane aquaglyceroporin that provides the main route for passive diffusional entry of this acid into the cell. Acetic acid stress transiently activates Hog1p mitogen-activated protein (MAP) kinase, which, in turn, phosphorylates Fps1p in order to target this channel for endocytosis and degradation in the vacuole. This activation of Hog1p is abolished with the loss of Fps1p, but is more sustained when cells express an open Fps1p channel refractory to destabilization. At neutral pH, much higher levels of acetate ( approximately 0.5 M) are needed to inhibit growth. Under such conditions, the loss of Fps1p does not abolish, but merely slows, the activation of Hog1p. Acetate stress also activates the Slt2(Mpk1)p cell integrity MAP kinase, possibly by causing inhibition of glucan synthase activity. In pH 4.5 cultures, this acetate activation of Slt2p is strongly enhanced by the loss of Fps1p and is dependent upon the cell surface sensor Wsc1p. Lack of Fps1p therefore exerts opposing effects on the activation of Hog1p and Slt2p in yeast exposed to acetic acid stress.
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Affiliation(s)
- Mehdi Mollapour
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Andrew Shepherd
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Peter W Piper
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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121
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Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments. Mol Syst Biol 2009; 5:287. [PMID: 19584836 PMCID: PMC2724975 DOI: 10.1038/msb.2009.45] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Accepted: 05/26/2009] [Indexed: 11/25/2022] Open
Abstract
Signaling cascades are triggered by environmental stimulation and propagate the signal to regulate transcription. Systematic reconstruction of the underlying regulatory mechanisms requires pathway-targeted, informative experimental data. However, practical experimental design approaches are still in their infancy. Here, we propose a framework that iterates design of experiments and identification of regulatory relationships downstream of a given pathway. The experimental design component, called MEED, aims to minimize the amount of laboratory effort required in this process. To avoid ambiguity in the identification of regulatory relationships, the choice of experiments maximizes diversity between expression profiles of genes regulated through different mechanisms. The framework takes advantage of expert knowledge about the pathways under study, formalized in a predictive logical model. By considering model-predicted dependencies between experiments, MEED is able to suggest a whole set of experiments that can be carried out simultaneously. Our framework was applied to investigate interconnected signaling pathways in yeast. In comparison with other approaches, MEED suggested the most informative experiments for unambiguous identification of transcriptional regulation in this system.
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122
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Alejandro-Osorio AL, Huebert DJ, Porcaro DT, Sonntag ME, Nillasithanukroh S, Will JL, Gasch AP. The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress. Genome Biol 2009; 10:R57. [PMID: 19470158 PMCID: PMC2718523 DOI: 10.1186/gb-2009-10-5-r57] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 05/13/2009] [Accepted: 05/26/2009] [Indexed: 12/20/2022] Open
Abstract
Chromatin-immunoprecipitation and computational analysis implicate Rpd3p as an important co-factor in the network of genes regulating the yeast environmental stress response. Background Yeast responding to stress activate a large gene expression program called the Environmental Stress Response that consists of approximately 600 repressed genes and approximately 300 induced genes. Numerous factors are implicated in regulating subsets of Environmental Stress Response genes; however, a complete picture of Environmental Stress Response regulation remains unclear. We investigated the role of the histone deacetylase Rpd3p, previously linked to the upstream regions of many Environmental Stress Response genes, in producing Environmental Stress Response gene expression changes in response to stress. Results We found that the Rpd3-Large complex is required for proper expression of both induced and repressed Environmental Stress Response genes under multiple stress conditions. Cells lacking RPD3 or the Rpd3-Large subunit PHO23 had a major defect in Environmental Stress Response initiation, particularly during the transient phase of expression immediately after stress exposure. Chromatin-immunoprecipitation showed a direct role for Rpd3-Large at representative genes; however, there were different effects on nucleosome occupancy and histone deacetylation at different promoters. Computational analysis implicated regulators that may act with Rpd3p at Environmental Stress Response genes. We provide genetic and biochemical evidence that Rpd3p is required for binding and action of the stress-activated transcription factor Msn2p, although the contribution of these factors differs for different genes. Conclusions Our results implicate Rpd3p as an important co-factor in the Environmental Stress Response regulatory network, and suggest the importance of histone modification in producing transient changes in gene expression triggered by stress.
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Affiliation(s)
- Adriana L Alejandro-Osorio
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, University Avenue, Madison, WI 53706, USA.
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123
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Pitoniak A, Birkaya B, Dionne HM, Vadaie N, Cullen PJ. The signaling mucins Msb2 and Hkr1 differentially regulate the filamentation mitogen-activated protein kinase pathway and contribute to a multimodal response. Mol Biol Cell 2009; 20:3101-14. [PMID: 19439450 DOI: 10.1091/mbc.e08-07-0760] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
A central question in the area of signal transduction is why pathways utilize common components. In the budding yeast Saccharomyces cerevisiae, the HOG and filamentous growth (FG) MAPK pathways require overlapping components but are thought to be induced by different stimuli and specify distinct outputs. To better understand the regulation of the FG pathway, we examined FG in one of yeast's native environments, the grape-producing plant Vitis vinifera. In this setting, different aspects of FG were induced in a temporal manner coupled to the nutrient cycle, which uncovered a multimodal feature of FG pathway signaling. FG pathway activity was modulated by the HOG pathway, which led to the finding that the signaling mucins Msb2p and Hkr1p, which operate at the head of the HOG pathway, differentially regulate the FG pathway. The two mucins exhibited different expression and secretion patterns, and their overproduction induced nonoverlapping sets of target genes. Moreover, Msb2p had a function in cell polarization through the adaptor protein Sho1p that Hkr1p did not. Differential MAPK activation by signaling mucins brings to light a new point of discrimination between MAPK pathways.
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Affiliation(s)
- Andrew Pitoniak
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14260-1300, USA
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124
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Luo F, Li B, Wan XF, Scheuermann RH. Core and periphery structures in protein interaction networks. BMC Bioinformatics 2009; 10 Suppl 4:S8. [PMID: 19426456 PMCID: PMC2681073 DOI: 10.1186/1471-2105-10-s4-s8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Characterizing the structural properties of protein interaction networks will help illuminate the organizational and functional relationships among elements in biological systems. RESULTS In this paper, we present a systematic exploration of the core/periphery structures in protein interaction networks (PINs). First, the concepts of cores and peripheries in PINs are defined. Then, computational methods are proposed to identify two types of cores, k-plex cores and star cores, from PINs. Application of these methods to a yeast protein interaction network has identified 110 k-plex cores and 109 star cores. We find that the k-plex cores consist of either "party" proteins, "date" proteins, or both. We also reveal that there are two classes of 1-peripheral proteins: "party" peripheries, which are more likely to be part of protein complex, and "connector" peripheries, which are more likely connected to different proteins or protein complexes. Our results also show that, besides connectivity, other variations in structural properties are related to the variation in biological properties. Furthermore, the negative correlation between evolutionary rate and connectivity are shown toysis. Moreover, the core/periphery structures help to reveal the existence of multiple levels of protein expression dynamics. CONCLUSION Our results show that both the structure and connectivity can be used to characterize topological properties in protein interaction networks, illuminating the functional organization of cellular systems.
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Affiliation(s)
- Feng Luo
- School of Computing, Clemson University, Clemson, SC, USA.
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125
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Glycosylation defects activate filamentous growth Kss1 MAPK and inhibit osmoregulatory Hog1 MAPK. EMBO J 2009; 28:1380-91. [PMID: 19369942 DOI: 10.1038/emboj.2009.104] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Accepted: 03/24/2009] [Indexed: 01/15/2023] Open
Abstract
The yeast filamentous growth (FG) MAP kinase (MAPK) pathway is activated under poor nutritional conditions. We found that the FG-specific Kss1 MAPK is activated by a combination of an O-glycosylation defect caused by disruption of the gene encoding the protein O-mannosyltransferase Pmt4, and an N-glycosylation defect induced by tunicamycin. The O-glycosylated membrane proteins Msb2 and Opy2 are both essential for activating the FG MAPK pathway, but only defective glycosylation of Msb2 activates the FG MAPK pathway. Although the osmoregulatory HOG (high osmolarity glycerol) MAPK pathway and the FG MAPK pathway share almost the entire upstream signalling machinery, osmostress activates only the HOG-specific Hog1 MAPK. Conversely, we now show that glycosylation defects activate only Kss1, while activated Kss1 and the Ptp2 tyrosine phosphatase inhibit Hog1. In the absence of Kss1 or Ptp2, however, glycosylation defects activate Hog1. When Hog1 is activated by glycosylation defects in ptp2 mutant, Kss1 activation is suppressed by Hog1. Thus, the reciprocal inhibitory loop between Kss1 and Hog1 allows only one or the other of these MAPKs to be stably activated under various stress conditions.
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126
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Rosonina E, Willis IM, Manley JL. Sub1 functions in osmoregulation and in transcription by both RNA polymerases II and III. Mol Cell Biol 2009; 29:2308-21. [PMID: 19204085 PMCID: PMC2663309 DOI: 10.1128/mcb.01841-08] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Revised: 01/12/2009] [Accepted: 01/29/2009] [Indexed: 11/20/2022] Open
Abstract
Sub1 is implicated in transcriptional activation, elongation, and mRNA 3'-end formation in budding yeast. To gain more insight into its function, we performed a synthetic genetic array screen with SUB1 that uncovered genetic interactions with genes involved in the high-osmolarity glycerol (HOG) osmoresponse pathway. We find that Sub1 and the HOG pathway are redundant for survival in moderate osmolarity. Chromatin immunoprecipitation analysis shows that Sub1 is recruited to osmoresponse gene promoters during osmotic shock and is required for full recruitment of TBP, TFIIB, and RNA polymerase II (RNAP II) at a subset of these genes. Furthermore, we detect Sub1 at the promoter of every constitutively transcribed RNAP II and, unexpectedly, at every RNAP III gene tested, but not at the RNAP I-transcribed ribosomal DNA promoter. Significantly, deletion of SUB1 reduced levels of promoter-associated RNAP II or III at these genes, but not TBP levels. Together these data suggest that, in addition to a general role in polymerase recruitment at constitutive RNAP II and RNAP III genes, during osmotic shock, Sub1 facilitates osmoresponse gene transcription by enhancing preinitiation complex formation.
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Affiliation(s)
- Emanuel Rosonina
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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127
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Fiedler D, Braberg H, Mehta M, Chechik G, Cagney G, Mukherjee P, Silva AC, Shales M, Collins SR, van Wageningen S, Kemmeren P, Holstege FCP, Weissman JS, Keogh MC, Koller D, Shokat KM, Krogan NJ. Functional organization of the S. cerevisiae phosphorylation network. Cell 2009; 136:952-63. [PMID: 19269370 DOI: 10.1016/j.cell.2008.12.039] [Citation(s) in RCA: 207] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Revised: 10/14/2008] [Accepted: 12/18/2008] [Indexed: 01/08/2023]
Abstract
Reversible protein phosphorylation is a signaling mechanism involved in all cellular processes. To create a systems view of the signaling apparatus in budding yeast, we generated an epistatic miniarray profile (E-MAP) comprised of 100,000 pairwise, quantitative genetic interactions, including virtually all protein and small-molecule kinases and phosphatases as well as key cellular regulators. Quantitative genetic interaction mapping reveals factors working in compensatory pathways (negative genetic interactions) or those operating in linear pathways (positive genetic interactions). We found an enrichment of positive genetic interactions between kinases, phosphatases, and their substrates. In addition, we assembled a higher-order map from sets of three genes that display strong interactions with one another: triplets enriched for functional connectivity. The resulting network view provides insights into signaling pathway regulation and reveals a link between the cell-cycle kinase, Cak1, the Fus3 MAP kinase, and a pathway that regulates chromatin integrity during transcription by RNA polymerase II.
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Affiliation(s)
- Dorothea Fiedler
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 94158, USA
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128
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García R, Rodríguez-Peña JM, Bermejo C, Nombela C, Arroyo J. The high osmotic response and cell wall integrity pathways cooperate to regulate transcriptional responses to zymolyase-induced cell wall stress in Saccharomyces cerevisiae. J Biol Chem 2009; 284:10901-11. [PMID: 19234305 DOI: 10.1074/jbc.m808693200] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The adaptation of Saccharomyces cerevisiae to situations in which cell wall integrity is seriously compromised mainly involves the cell wall integrity (CWI) pathway. However, in a recent work ( Bermejo, C., Rodriguez, E., García, R., Rodríguez-Peña, J. M., Rodríguez de la Concepción, M. L., Rivas, C., Arias, P., Nombela, C., Posas, F., and Arroyo, J. (2008) Mol. Biol. Cell 19, 1113-1124 ) we have demonstrated the co-participation of the high osmotic response (HOG) pathway to ensure yeast survival to cell wall stress mediated by zymolyase, which hydrolyzes the beta-1,3 glucan network. Here we have characterized the role of both pathways in the regulation of the overall yeast transcriptional responses to zymolyase treatment using whole genome expression profiling. A main group of yeast genes is dependent on both MAPKs, Slt2 and Hog1, for their induction. The transcriptional activation of these genes depends on the MAPKKK Bck1, the transcription factor Rlm1, and elements of the sho1 branch of the HOG pathway, but not on the sensors of the CWI pathway. A second group of genes is dependent on Slt2 but not Hog1 or Pbs2. However, the induction of these genes is dependent on upstream elements of the HOG pathway such as Sho1, Ste50, and Ste11, in accordance with a sequential activation of the HOG and CWI pathways. Zymolyase also promotes an osmotic-like transcriptional response with the activation of a group of genes dependent on elements of the Sho1 branch of HOG pathway but not on Slt2, with the induction of many of them dependent on Msn2/4. Additionally, in the absence of Hog1, zymolyase induces an alternative response related to mating and filamentation as a consequence of the cross-talk between these pathways and the HOG pathway. Finally, in the absence of Slt2, zymolyase increases the induction of genes associated with osmotic adaptation with respect to the wild type, suggesting an inhibitory effect of the CWI pathway over the HOG pathway. These studies clearly reveal the complexity of the signal transduction machinery responsible for regulating yeast adaptation responses to cell wall stress.
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Affiliation(s)
- Raúl García
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
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129
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Hog1 mitogen-activated protein kinase (MAPK) interrupts signal transduction between the Kss1 MAPK and the Tec1 transcription factor to maintain pathway specificity. EUKARYOTIC CELL 2009; 8:606-16. [PMID: 19218425 DOI: 10.1128/ec.00005-09] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In Saccharomyces cerevisiae, the mating, filamentous growth (FG), and high-osmolarity glycerol (HOG) mitogen-activated protein kinase (MAPK) signaling pathways share components and yet mediate distinct responses to different extracellular signals. Cross talk is suppressed between the mating and FG pathways because mating signaling induces the destruction of the FG transcription factor Tec1. We show here that HOG pathway activation results in phosphorylation of the FG MAPK, Kss1, and the MAPKK, Ste7. However, FG transcription is not activated because HOG signaling prevents the activation of Tec1. In contrast to the mating pathway, we find that the mechanism involves the inhibition of DNA binding by Tec1 rather than its destruction. We also find that nuclear accumulation of Tec1 is not affected by HOG signaling. Inhibition by Hog1 is apparently indirect since it does not require any of the consensus S/TP MAPK phosphorylation sites on Tec1, its DNA-binding partner Ste12, or the associated regulators Dig1 or Dig2. It also does not require the consensus MAPK sites of the Ste11 activator Ste50, in contrast to a recent proposal for a role for negative feedback in specificity. Our results demonstrate that HOG signaling interrupts the FG pathway signal transduction between the phosphorylation of Kss1 and the activation of DNA binding by Tec1.
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130
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Halperin Y, Linhart C, Ulitsky I, Shamir R. Allegro: analyzing expression and sequence in concert to discover regulatory programs. Nucleic Acids Res 2009; 37:1566-79. [PMID: 19151090 PMCID: PMC2655690 DOI: 10.1093/nar/gkn1064] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A major goal of system biology is the characterization of transcription factors and microRNAs (miRNAs) and the transcriptional programs they regulate. We present Allegro, a method for de-novo discovery of cis-regulatory transcriptional programs through joint analysis of genome-wide expression data and promoter or 3' UTR sequences. The algorithm uses a novel log-likelihood-based, non-parametric model to describe the expression pattern shared by a group of co-regulated genes. We show that Allegro is more accurate and sensitive than existing techniques, and can simultaneously analyze multiple expression datasets with more than 100 conditions. We apply Allegro on datasets from several species and report on the transcriptional modules it uncovers. Our analysis reveals a novel motif over-represented in the promoters of genes highly expressed in murine oocytes, and several new motifs related to fly development. Finally, using stem-cell expression profiles, we identify three miRNA families with pivotal roles in human embryogenesis.
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Affiliation(s)
- Yonit Halperin
- School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
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131
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Soufi B, Kelstrup CD, Stoehr G, Fröhlich F, Walther TC, Olsen JV. Global analysis of the yeast osmotic stress response by quantitative proteomics. MOLECULAR BIOSYSTEMS 2009; 5:1337-46. [DOI: 10.1039/b902256b] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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132
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Hersen P, McClean M, Ramanathan S. [Dynamic analysis of cell signalling: the example of the Saccharomyces cerevisiae osmotic response]. Med Sci (Paris) 2009; 24:1020-2. [PMID: 19116106 DOI: 10.1051/medsci/200824121020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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133
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Structure and function of a transcriptional network activated by the MAPK Hog1. Nat Genet 2008; 40:1300-6. [PMID: 18931682 PMCID: PMC2825711 DOI: 10.1038/ng.235] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2008] [Accepted: 08/13/2008] [Indexed: 11/09/2022]
Abstract
Cells regulate gene expression using a complex network of signaling pathways, transcription factors and promoters. To gain insight into the structure and function of these networks, we analyzed gene expression in single- and multiple-mutant strains to build a quantitative model of the Hog1 MAPK-dependent osmotic stress response in budding yeast. Our model reveals that the Hog1 and general stress (Msn2/4) pathways interact, at both the signaling and promoter level, to integrate information and create a context-dependent response. This study lays out a path to identifying and characterizing the role of signal integration and processing in other gene regulatory networks.
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134
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Stress resistance and signal fidelity independent of nuclear MAPK function. Proc Natl Acad Sci U S A 2008; 105:12212-7. [PMID: 18719124 DOI: 10.1073/pnas.0805797105] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Elevated external solute stimulates a conserved MAPK cascade that elicits responses that maintain osmotic balance. The yeast high-osmolarity glycerol (HOG) pathway activates Hog1 MAPK (mammalian ortholog p38alpha/SAPKalpha), which enters the nucleus and induces expression of >50 genes, implying that transcriptional up-regulation is necessary to cope with hyperosmotic stress. Contrary to this expectation, we show here that cells lacking the karyopherin required for Hog1 nuclear import or in which Hog1 is anchored at the plasma membrane (or both) can withstand long-term hyperosmotic challenge by ionic and nonionic solutes without exhibiting the normal change in transcriptional program (comparable with hog1Delta cells), as judged by mRNA hybridization and microarray analysis. For such cells to survive hyperosmotic stress, systematic genetic analysis ruled out the need for any Hog1-dependent transcription factor, the Hog1-activated MAPKAP kinases, or ion, glycerol, and water channels. By contrast, enzymes needed for glycerol production were essential for viability. Thus, control of intracellular glycerol formation by Hog1 is critical for maintenance of osmotic balance but not transcriptional induction of any gene.
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135
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Melamed D, Pnueli L, Arava Y. Yeast translational response to high salinity: global analysis reveals regulation at multiple levels. RNA (NEW YORK, N.Y.) 2008; 14:1337-51. [PMID: 18495938 PMCID: PMC2441982 DOI: 10.1261/rna.864908] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2007] [Accepted: 03/27/2008] [Indexed: 05/23/2023]
Abstract
Genome-wide studies of steady-state mRNA levels revealed common principles underlying transcriptional changes in response to external stimuli. To uncover principles that govern other stages of the gene-expression response, we analyzed the translational response and its coordination with transcriptome changes following exposure to severe stress. Yeast cells were grown for 1 h in medium containing 1 M NaCl, which elicits a maximal but transient translation inhibition, and nonpolysomal or polysomal mRNA pools were subjected to DNA-microarray analyses. We observed a strong repression in polysomal association for most mRNAs, with no simple correlation with the changes in transcript levels. This led to an apparent accumulation of many mRNAs as a nontranslating pool, presumably waiting for recovery from the stress. However, some mRNAs demonstrated a correlated change in their polysomal association and their transcript levels (i.e., potentiation). This group was enriched with targets of the transcription factors Msn2/Msn4, and the translational induction of several tested mRNAs was diminished in an Msn2/Msn4 deletion strain. Genome-wide analysis of a strain lacking the high salinity response kinase Hog1p revealed that the group of translationally affected genes is significantly enriched with motifs that were shown to be associated with the ARE-binding protein Pub1. Since a relatively small number of genes was affected by Hog1p deletion, additional signaling pathways are likely to be involved in coordinating the translational response to severe salinity stress.
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Affiliation(s)
- Daniel Melamed
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
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136
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Abstract
MOTIVATION The availability of genome-scale data has enabled an abundance of novel analysis techniques for investigating a variety of systems-level biological relationships. As thousands of such datasets become available, they provide an opportunity to study high-level associations between cellular pathways and processes. This also allows the exploration of shared functional enrichments between diverse biological datasets, and it serves to direct experimenters to areas of low data coverage or with high probability of new discoveries. RESULTS We analyze the functional structure of Saccharomyces cerevisiae datasets from over 950 publications in the context of over 140 biological processes. This includes a coverage analysis of biological processes given current high-throughput data, a data-driven map of associations between processes, and a measure of similar functional activity between genome-scale datasets. This uncovers subtle gene expression similarities in three otherwise disparate microarray datasets due to a shared strain background. We also provide several means of predicting areas of yeast biology likely to benefit from additional high-throughput experimental screens. AVAILABILITY Predictions are provided in supplementary tables; software and additional data are available from the authors by request. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- C Huttenhower
- Department of Computer Science, Princeton University, 35 Olden Street, Princeton, NJ 08540, USA
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137
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Abstract
Signaling pathways relay information about changes in the external environment so that cells can respond appropriately. How much information a pathway can carry depends on its bandwidth. We designed a microfluidic device to reliably change the environment of single cells over a range of frequencies. Using this device, we measured the bandwidth of the Saccharomyces cerevisiae signaling pathway that responds to high osmolarity. This prototypical pathway, the HOG pathway, is shown to act as a low-pass filter, integrating the signal when it changes rapidly and following it faithfully when it changes more slowly. We study the dependence of the pathway's bandwidth on its architecture. We measure previously unknown bounds on all of the in vivo reaction rates acting in this pathway. We find that the two-component Ssk1 branch of this pathway is capable of fast signal integration, whereas the kinase Ste11 branch is not. Our experimental techniques can be applied to other signaling pathways, allowing the measurement of their in vivo kinetics and the quantification of their information capacity.
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138
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Mollapour M, Shepherd A, Piper PW. Novel stress responses facilitate Saccharomyces cerevisiae growth in the presence of the monocarboxylate preservatives. Yeast 2008; 25:169-77. [PMID: 18240334 DOI: 10.1002/yea.1576] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Certain yeasts are relatively resistant to the small number of monocarboxylic acids allowed in food preservation, with the result that these preservatives often have to be used in high concentrations in order to prevent spoilage. When grown at slightly acid pH, Saccharomyces cerevisiae acquires elevated resistance to these acids by means of discrete stress responses. Acquisition of resistance to acetic acid involves loss of Fps1p, the aquaglyceroporin of the plasma membrane that facilitates the passive diffusional entry of this acid into cells. Acetic acid stress transiently activates Hog1p mitogen-activated protein kinase, which then directly phosphorylates Fps1p in order to target this channel for endocytosis and degradation in the vacuole. Other carboxylate preservatives (propionate, sorbate or benzoate) are too large to traverse the Fps1p pore. Instead, being more lipophilic than acetic acid, they enter cells mainly by a process of non-facilitated diffusion across the plasma membrane. Once inside the cell, these acids activate War1p, a transcription factor that induces the gene for the Pdr12p plasma membrane ATP-binding cassette transporter. Pdr12p lowers the intracellular levels of propionate, sorbate or benzoate by catalysing the active efflux of the preservative anion from the cell. Still other mechanisms of weak acid resistance are found in Zygosaccharomyces, including a capacity for the oxidative degradation of sorbic and benzoic acids conferred by a mitochondrial monooxygenase, a system absent in S. cerevisiae.
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Affiliation(s)
- Mehdi Mollapour
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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139
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Pan Z, Agarwal AK, Xu T, Feng Q, Baerson SR, Duke SO, Rimando AM. Identification of molecular pathways affected by pterostilbene, a natural dimethylether analog of resveratrol. BMC Med Genomics 2008; 1:7. [PMID: 18366703 PMCID: PMC2330146 DOI: 10.1186/1755-8794-1-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Accepted: 03/20/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pterostilbene, a naturally occurring phenolic compound produced by agronomically important plant genera such as Vitis and Vacciunium, is a phytoalexin exhibiting potent antifungal activity. Additionally, recent studies have demonstrated several important pharmacological properties associated with pterostilbene. Despite this, a systematic study of the effects of pterostilbene on eukaryotic cells at the molecular level has not been previously reported. Thus, the aim of the present study was to identify the cellular pathways affected by pterostilbene by performing transcript profiling studies, employing the model yeast Saccharomyces cerevisiae. METHODS S. cerevisiae strain S288C was exposed to pterostilbene at the IC50 concentration (70 muM) for one generation (3 h). Transcript profiling experiments were performed on three biological replicate samples using the Affymetrix GeneChip Yeast Genome S98 Array. The data were analyzed using the statistical methods available in the GeneSifter microarray data analysis system. To validate the results, eleven differentially expressed genes were further examined by quantitative real-time RT-PCR, and S. cerevisiae mutant strains with deletions in these genes were analyzed for altered sensitivity to pterostilbene. RESULTS Transcript profiling studies revealed that pterostilbene exposure significantly down-regulated the expression of genes involved in methionine metabolism, while the expression of genes involved in mitochondrial functions, drug detoxification, and transcription factor activity were significantly up-regulated. Additional analyses revealed that a large number of genes involved in lipid metabolism were also affected by pterostilbene treatment. CONCLUSION Using transcript profiling, we have identified the cellular pathways targeted by pterostilbene, an analog of resveratrol. The observed response in lipid metabolism genes is consistent with its known hypolipidemic properties, and the induction of mitochondrial genes is consistent with its demonstrated role in apoptosis in human cancer cell lines. Furthermore, our data show that pterostilbene has a significant effect on methionine metabolism, a previously unreported effect for this compound.
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Affiliation(s)
- Zhiqiang Pan
- United States Department of Agriculture, Agricultural Research Service, Natural Products Utilization Research Unit, University, Mississippi 38677, USA
| | - Ameeta K Agarwal
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, 38677, USA
| | - Tao Xu
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, 38677, USA
| | - Qin Feng
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, 38677, USA
| | - Scott R Baerson
- United States Department of Agriculture, Agricultural Research Service, Natural Products Utilization Research Unit, University, Mississippi 38677, USA
| | - Stephen O Duke
- United States Department of Agriculture, Agricultural Research Service, Natural Products Utilization Research Unit, University, Mississippi 38677, USA
| | - Agnes M Rimando
- United States Department of Agriculture, Agricultural Research Service, Natural Products Utilization Research Unit, University, Mississippi 38677, USA
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140
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Abstract
Unicellular fungi thrive in diverse niches around the world, and many of these niches present unique and stressful challenges that must be contended with by their inhabitants. Numerous studies have investigated the genomic expression responses to environmental stress in 'model' ascomycete fungi, including Saccharomyces cerevisiae, Candida albicans and Schizosaccharomyces pombe. This review presents a comparative-genomics perspective on the environmental stress response, a common response to diverse stresses. Implications for the role of this response, based on its presence or absence in fungi from disparate ecological niches, are discussed.
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Affiliation(s)
- Audrey P Gasch
- Laboratory of Genetics and Genome Center of Wisconsin, University of Wisconsin Madison, Madison, WI 53706, USA.
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141
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Del Vescovo V, Casagrande V, Bianchi MM, Piccinni E, Frontali L, Militti C, Fardeau V, Devaux F, Sanza CD, Presutti C, Negri R. Role of Hog1 and Yaf9 in the transcriptional response ofSaccharomyces cerevisiaeto cesium chloride. Physiol Genomics 2008; 33:110-20. [DOI: 10.1152/physiolgenomics.00251.2007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We analyzed the global transcriptional response of Saccharomyces cerevisiae cells exposed to different concentrations of CsCl in the growth medium and at different times after addition. Early responsive genes were mainly involved in cell wall structure and biosynthesis. About half of the induced genes were previously shown to respond to other alkali metal cations in a Hog1-dependent fashion. Western blot analysis confirmed that cesium concentrations as low as 100 mM activate Hog1 phosphorylation. Another important fraction of the cesium-modulated genes requires Yaf9p for full responsiveness as shown by the transcriptome of a yaf9-deleted strain in the presence of cesium. We showed that a cell wall-restructuring process promptly occurs in response to cesium addition, which is dependent on the presence of both Hog1 and Yaf9 proteins. Moreover, the sensitivity to low concentration of cesium of the yaf9-deleted strain is not observed in a strain carrying the hog1/ yaf9 double deletion. We conclude that the observed early transcriptional modulation of cell wall genes has a crucial role in S. cerevisiae adaptation to cesium.
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Affiliation(s)
- Valerio Del Vescovo
- Istituto Pasteur Fondazione Cenci-Bolognetti, Dipartimento di Biologia Cellulare e dello Sviluppo, Università degli Studi di Roma, La Sapienza, Rome, Italy
| | - Viviana Casagrande
- Istituto Pasteur Fondazione Cenci-Bolognetti, Dipartimento di Biologia Cellulare e dello Sviluppo, Università degli Studi di Roma, La Sapienza, Rome, Italy
| | - Michele M. Bianchi
- Istituto Pasteur Fondazione Cenci-Bolognetti, Dipartimento di Biologia Cellulare e dello Sviluppo, Università degli Studi di Roma, La Sapienza, Rome, Italy
| | - Eugenia Piccinni
- Istituto Pasteur Fondazione Cenci-Bolognetti, Dipartimento di Biologia Cellulare e dello Sviluppo, Università degli Studi di Roma, La Sapienza, Rome, Italy
| | - Laura Frontali
- Istituto Pasteur Fondazione Cenci-Bolognetti, Dipartimento di Biologia Cellulare e dello Sviluppo, Università degli Studi di Roma, La Sapienza, Rome, Italy
- Laboratory of Functional Genomics and Proteomics of Model Systems, University of Rome, La Sapienza, Rome, Italy
| | - Cristina Militti
- Istituto Pasteur Fondazione Cenci-Bolognetti, Dipartimento di Biologia Cellulare e dello Sviluppo, Università degli Studi di Roma, La Sapienza, Rome, Italy
| | - Vivienne Fardeau
- Laboratoire de Génomique CNRS, Ecole Normale Supérieure, Paris, France
| | - Frédéric Devaux
- Laboratoire de Génomique CNRS, Ecole Normale Supérieure, Paris, France
| | - Claudio Di Sanza
- Dipartimento di Genetica e Biologia Molecolare, Università degli Studi di Roma, La Sapienza
| | - Carlo Presutti
- Dipartimento di Genetica e Biologia Molecolare, Università degli Studi di Roma, La Sapienza
- Laboratory of Functional Genomics and Proteomics of Model Systems, University of Rome, La Sapienza, Rome, Italy
| | - Rodolfo Negri
- Istituto Pasteur Fondazione Cenci-Bolognetti, Dipartimento di Biologia Cellulare e dello Sviluppo, Università degli Studi di Roma, La Sapienza, Rome, Italy
- Laboratory of Functional Genomics and Proteomics of Model Systems, University of Rome, La Sapienza, Rome, Italy
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142
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Vinod PK, Sengupta N, Bhat PJ, Venkatesh KV. Integration of global signaling pathways, cAMP-PKA, MAPK and TOR in the regulation of FLO11. PLoS One 2008; 3:e1663. [PMID: 18301741 PMCID: PMC2246015 DOI: 10.1371/journal.pone.0001663] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Accepted: 01/22/2008] [Indexed: 11/19/2022] Open
Abstract
The budding yeast, Saccharomyces cerevisiae, responds to various environmental cues by invoking specific adaptive mechanisms for their survival. Under nitrogen limitation, S. cerevisiae undergoes a dimorphic filamentous transition called pseudohyphae, which helps the cell to forage for nutrients and reach an environment conducive for growth. This transition is governed by a complex network of signaling pathways, namely cAMP-PKA, MAPK and TOR, which controls the transcriptional activation of FLO11, a flocculin gene that encodes a cell wall protein. However, little is known about how these pathways co-ordinate to govern the conversion of nutritional availability into gene expression. Here, we have analyzed an integrative network comprised of cAMP-PKA, MAPK and TOR pathways with respect to the availability of nitrogen source using experimental and steady state modeling approach. Our experiments demonstrate that the steady state expression of FLO11 was bistable over a range of inducing ammonium sulphate concentration based on the preculturing condition. We also show that yeast switched from FLO11 expression to accumulation of trehalose, a STRE response controlled by a transcriptional activator Msn2/4, with decrease in the inducing concentration to complete starvation. Steady state analysis of the integrative network revealed the relationship between the environment, signaling cascades and the expression of FLO11. We demonstrate that the double negative feedback loop in TOR pathway can elicit a bistable response, to differentiate between vegetative growth, filamentous growth and STRE response. Negative feedback on TOR pathway function to restrict the expression of FLO11 under nitrogen starved condition and also with re-addition of nitrogen to starved cells. In general, we show that these global signaling pathways respond with specific sensitivity to regulate the expression of FLO11 under nitrogen limitation. The holistic steady state modeling approach of the integrative network revealed how the global signaling pathways could differentiate between multiple phenotypes.
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Affiliation(s)
- P. K. Vinod
- School of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, India
| | - Neelanjan Sengupta
- Department of Chemical Engineering, Indian Institute of Technology, Bombay, Powai, Mumbai, India
| | - P. J. Bhat
- School of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, India
| | - K. V. Venkatesh
- School of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, India
- Department of Chemical Engineering, Indian Institute of Technology, Bombay, Powai, Mumbai, India
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143
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Bermejo C, Rodríguez E, García R, Rodríguez-Peña JM, Rodríguez de la Concepción ML, Rivas C, Arias P, Nombela C, Posas F, Arroyo J. The sequential activation of the yeast HOG and SLT2 pathways is required for cell survival to cell wall stress. Mol Biol Cell 2008; 19:1113-24. [PMID: 18184748 DOI: 10.1091/mbc.e07-08-0742] [Citation(s) in RCA: 164] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Yeast mitogen-activated protein kinase (MAPK) signaling pathways transduce external stimuli into cellular responses very precisely. The MAPKs Slt2/Mpk1 and Hog1 regulate transcriptional responses of adaptation to cell wall and osmotic stresses, respectively. Unexpectedly, we observe that the activation of a cell wall integrity (CWI) response to the cell wall damage caused by zymolyase (beta-1,3 glucanase) requires both the HOG and SLT2 pathways. Zymolyase activates both MAPKs and Slt2 activation depends on the Sho1 branch of the HOG pathway under these conditions. Moreover, adaptation to zymolyase requires essential components of the CWI pathway, namely the redundant MAPKKs Mkk1/Mkk2, the MAPKKK Bck1, and Pkc1, but it does not require upstream elements, including the sensors and the guanine nucleotide exchange factors of this pathway. In addition, the transcriptional activation of genes involved in adaptation to cell wall stress, like CRH1, depends on the transcriptional factor Rlm1 regulated by Slt2, but not on the transcription factors regulated by Hog1. Consistent with these findings, both MAPK pathways are essential for cell survival under these circumstances because mutant strains deficient in different components of both pathways are hypersensitive to zymolyase. Thus, a sequential activation of two MAPK pathways is required for cellular adaptation to cell wall damage.
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Affiliation(s)
- Clara Bermejo
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
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144
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Zou X, Peng T, Pan Z. Modeling specificity in the yeast MAPK signaling networks. J Theor Biol 2008; 250:139-55. [DOI: 10.1016/j.jtbi.2007.09.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Revised: 09/18/2007] [Accepted: 09/18/2007] [Indexed: 02/03/2023]
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145
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Behar M, Dohlman HG, Elston TC. Kinetic insulation as an effective mechanism for achieving pathway specificity in intracellular signaling networks. Proc Natl Acad Sci U S A 2007; 104:16146-51. [PMID: 17913886 PMCID: PMC2042176 DOI: 10.1073/pnas.0703894104] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intracellular signaling pathways that share common components often elicit distinct physiological responses. In most cases, the biochemical mechanisms responsible for this signal specificity remain poorly understood. Protein scaffolds and cross-inhibition have been proposed as strategies to prevent unwanted cross-talk. Here, we report a mechanism for signal specificity termed "kinetic insulation." In this approach signals are selectively transmitted through the appropriate pathway based on their temporal profile. In particular, we demonstrate how pathway architectures downstream of a common component can be designed to efficiently separate transient signals from signals that increase slowly over time. Furthermore, we demonstrate that upstream signaling proteins can generate the appropriate input to the common pathway component regardless of the temporal profile of the external stimulus. Our results suggest that multilevel signaling cascades may have evolved to modulate the temporal profile of pathway activity so that stimulus information can be efficiently encoded and transmitted while ensuring signal specificity.
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Affiliation(s)
- Marcelo Behar
- Departments of Physics
- Program in Cellular and Molecular Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | | | - Timothy C. Elston
- Pharmacology, and
- To whom correspondence should be addressed. E-mail:
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146
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Cheetham J, Smith DA, da Silva Dantas A, Doris KS, Patterson MJ, Bruce CR, Quinn J. A single MAPKKK regulates the Hog1 MAPK pathway in the pathogenic fungus Candida albicans. Mol Biol Cell 2007; 18:4603-14. [PMID: 17804815 PMCID: PMC2043575 DOI: 10.1091/mbc.e07-06-0581] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The Hog1 mitogen-activated protein kinase (MAPK) plays a central role in stress responses in the human pathogen Candida albicans. Here, we have investigated the MAPK kinase kinase (MAPKKK)-dependent regulation of the pathway. In contrast to the Hog1 pathway in Saccharomyces cerevisiae, which is regulated by three MAPKKKs (Ssk2, Ssk22, and Ste11), our results demonstrate that Hog1 in C. albicans is regulated by a single MAPKKK Ssk2. Deletion of SSK2 results in comparable stress and morphological phenotypes exhibited by hog1Delta cells, and Ssk2 is required for the stress-induced phosphorylation and nuclear accumulation of Hog1, and for Hog1-dependent gene expression. Furthermore, phenotypes associated with deletion of SSK2 can be circumvented by expression of a phosphomimetic mutant of the MAPKK Pbs2, indicating that Ssk2 regulates Hog1 via activation of Pbs2. In S. cerevisiae, the Hog1 pathway is also regulated by the MAPKKK Ste11. However, we can find no connection between Ste11 and the regulation of Hog1 in C. albicans. Furthermore, expression of a chimeric Pbs2 protein containing the Ste11-dependent regulatory region of S. cerevisiae Pbs2, fails to stimulate Ste11-dependent stress signaling in C. albicans. Collectively, our data show that Ssk2 is the sole MAPKKK to relay stress signals to Hog1 in C. albicans and that the MAPK signaling network in C. albicans has diverged significantly from the corresponding network in S. cerevisiae.
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Affiliation(s)
- Jill Cheetham
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Deborah A. Smith
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Alessandra da Silva Dantas
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Kathryn S. Doris
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Miranda J. Patterson
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Catherine R. Bruce
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Janet Quinn
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
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147
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Gregori C, Schüller C, Roetzer A, Schwarzmüller T, Ammerer G, Kuchler K. The high-osmolarity glycerol response pathway in the human fungal pathogen Candida glabrata strain ATCC 2001 lacks a signaling branch that operates in baker's yeast. EUKARYOTIC CELL 2007; 6:1635-45. [PMID: 17616630 PMCID: PMC2043364 DOI: 10.1128/ec.00106-07] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Accepted: 06/26/2007] [Indexed: 01/26/2023]
Abstract
The high-osmolarity glycerol (HOG) mitogen-activated protein (MAP) kinase pathway mediates adaptation to high-osmolarity stress in the yeast Saccharomyces cerevisiae. Here we investigate the function of HOG in the human opportunistic fungal pathogen Candida glabrata. C. glabrata sho1Delta (Cgsho1Delta) deletion strains from the sequenced ATCC 2001 strain display severe growth defects under hyperosmotic conditions, a phenotype not observed for yeast sho1Delta mutants. However, deletion of CgSHO1 in other genetic backgrounds fails to cause osmostress hypersensitivity, whereas cells lacking the downstream MAP kinase Pbs2 remain osmosensitive. Notably, ATCC 2001 Cgsho1Delta cells also display methylglyoxal hypersensitivity, implying the inactivity of the Sln1 branch in ATCC 2001. Genomic sequencing of CgSSK2 in different C. glabrata backgrounds demonstrates that ATCC 2001 harbors a truncated and mutated Cgssk2-1 allele, the only orthologue of yeast SSK2/SSK22 genes. Thus, the osmophenotype of ATCC 2001 is caused by a point mutation in Cgssk2-1, which debilitates the second HOG pathway branch. Functional complementation experiments unequivocally demonstrate that HOG signaling in yeast and C. glabrata share similar functions in osmostress adaptation. In contrast to yeast, however, Cgsho1Delta mutants display hypersensitivity to weak organic acids such as sorbate and benzoate. Hence, CgSho1 is also implicated in modulating weak acid tolerance, suggesting that HOG signaling in C. glabrata mediates the response to multiple stress conditions.
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Affiliation(s)
- Christa Gregori
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University Vienna, ,Dr. Bohr-Gasse 9/2, A-1030 Vienna, Austria
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148
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Kelley JB, Paschal BM. Hyperosmotic stress signaling to the nucleus disrupts the Ran gradient and the production of RanGTP. Mol Biol Cell 2007; 18:4365-76. [PMID: 17761537 PMCID: PMC2043571 DOI: 10.1091/mbc.e07-01-0089] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The RanGTP gradient depends on nucleocytoplasmic shuttling of Ran and its nucleotide exchange in the nucleus. Here we show that hyperosmotic stress signaling induced by sorbitol disrupts the Ran protein gradient and reduces the production of RanGTP. Ran gradient disruption is rapid and is followed by early (10-20 min) and late (30-60 min) phases of recovery. Results from SB203580 and siRNA experiments suggest the stress kinase p38 is important for Ran gradient recovery. NTF2 and Mog1, which are transport factors that regulate the nuclear localization of Ran, showed kinetics of delocalization and recovery similar to Ran. Microinjection of a nuclear localization signal reporter protein revealed that sorbitol stress decreases the rate of nuclear import. Sorbitol stress also slowed RCC1 mobility in the nucleus, which is predicted to reduce RCC1 dissociation from chromatin and RanGTP production. This was tested using a FRET biosensor that registers nuclear RanGTP levels, which were reduced in response to sorbitol stress. Although sorbitol alters nucleotide levels, we show that inverting the GTP/GDP ratio in cells is not sufficient to disrupt the Ran gradient. Thus, the Ran system is a target of hyperosmotic stress signaling, and cells use protein localization-based mechanisms as part of a rapid stress response.
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Affiliation(s)
- Joshua B. Kelley
- Center for Cell Signaling, Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Bryce M. Paschal
- Center for Cell Signaling, Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
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149
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Biswas S, Van Dijck P, Datta A. Environmental sensing and signal transduction pathways regulating morphopathogenic determinants of Candida albicans. Microbiol Mol Biol Rev 2007; 71:348-76. [PMID: 17554048 PMCID: PMC1899878 DOI: 10.1128/mmbr.00009-06] [Citation(s) in RCA: 396] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Candida albicans is an opportunistic fungal pathogen that is found in the normal gastrointestinal flora of most healthy humans. However, under certain environmental conditions, it can become a life-threatening pathogen. The shift from commensal organism to pathogen is often correlated with the capacity to undergo morphogenesis. Indeed, under certain conditions, including growth at ambient temperature, the presence of serum or N-acetylglucosamine, neutral pH, and nutrient starvation, C. albicans can undergo reversible transitions from the yeast form to the mycelial form. This morphological plasticity reflects the interplay of various signal transduction pathways, either stimulating or repressing hyphal formation. In this review, we provide an overview of the different sensing and signaling pathways involved in the morphogenesis and pathogenesis of C. albicans. Where appropriate, we compare the analogous pathways/genes in Saccharomyces cerevisiae in an attempt to highlight the evolution of the different components of the two organisms. The downstream components of these pathways, some of which may be interesting antifungal targets, are also discussed.
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Affiliation(s)
- Subhrajit Biswas
- National Centre for Plant Genome Research, New Delhi 110 067, India
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150
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Vaupotič T, Plemenitaš A. Differential gene expression and Hog1 interaction with osmoresponsive genes in the extremely halotolerant black yeast Hortaea werneckii. BMC Genomics 2007; 8:280. [PMID: 17705830 PMCID: PMC2034391 DOI: 10.1186/1471-2164-8-280] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Accepted: 08/16/2007] [Indexed: 11/16/2022] Open
Abstract
Background Fluctuations in external salinity force eukaryotic cells to respond by changes in the gene expression of proteins acting in protective biochemical processes, thus counteracting the changing osmotic pressure. The high-osmolarity glycerol (HOG) signaling pathway is essential for the efficient up-regulation of the osmoresponsive genes. In this study, the differential gene expression of the extremely halotolerant black yeast Hortaea werneckii was explored. Furthermore, the interaction of mitogen-activated protein kinase HwHog1 and RNA polymerase II with the chromatin in cells adapted to an extremely hypersaline environment was analyzed. Results A cDNA subtraction library was constructed for H. werneckii, adapted to moderate salinity or an extremely hypersaline environment of 4.5 M NaCl. An uncommon osmoresponsive set of 95 differentially expressed genes was identified. The majority of these had not previously been connected with the adaptation of salt-sensitive S. cerevisiae to hypersaline conditions. The transcriptional response in hypersaline-adapted and hypersaline-stressed cells showed that only a subset of the identified genes responded to acute salt-stress, whereas all were differentially expressed in adapted cells. Interaction with HwHog1 was shown for 36 of the 95 differentially expressed genes. The majority of the identified osmoresponsive and HwHog1-dependent genes in H. werneckii have not been previously reported as Hog1-dependent genes in the salt-sensitive S. cerevisiae. The study further demonstrated the co-occupancy of HwHog1 and RNA polymerase II on the chromatin of 17 up-regulated and 2 down-regulated genes in 4.5 M NaCl-adapted H. werneckii cells. Conclusion Extremely halotolerant H. werneckii represents a suitable and highly relevant organism to study cellular responses to environmental salinity. In comparison with the salt-sensitive S. cerevisiae, this yeast shows a different set of genes being expressed at high salt concentrations and interacting with HwHog1 MAP kinase, suggesting atypical processes deserving of further study.
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Affiliation(s)
- Tomaž Vaupotič
- Institute of Biochemistry, University of Ljubljana Faculty of Medicine, Vrazov Trg 2, SI-1000 Ljubljana, Slovenia
| | - Ana Plemenitaš
- Institute of Biochemistry, University of Ljubljana Faculty of Medicine, Vrazov Trg 2, SI-1000 Ljubljana, Slovenia
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