Inferring Stress Activated Signaling Networks In Saccharomyces Cerevisiae Reveals Complex Pathway Integration
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Inferring Stress Activated Signaling Networks In Saccharomyces Cerevisiae Reveals Complex Pathway Integration
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Author : Matthew Edward MacGilvray
language : en
Publisher:
Release Date : 2017
Inferring Stress Activated Signaling Networks In Saccharomyces Cerevisiae Reveals Complex Pathway Integration written by Matthew Edward MacGilvray and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with categories.
Cells respond to stressful conditions by coordinating a complex, multi-faceted response that spans many levels of physiology. Much of the response is coordinated by changes in protein phosphorylation. Although the regulators of transcriptome changes during stress are well characterized in Saccharomyces cerevisiae, the upstream regulatory network controlling protein phosphorylation is less well dissected. In this thesis, we developed a computational approach to infer the stress-activated signaling network that regulates phosphorylation changes in response to salt stress and the ER stressor dithiothreitol (DTT). The method uses integer linear programming (ILP) to integrate stress-responsive phospho-proteome responses in wild-type and mutant strains, predicted phosphorylation motifs on groups of coregulated peptides, and published protein interaction data. The inferred salt-network predicted new regulatory connections between stress-activated and growth-regulating pathways and suggested mechanisms coordinating metabolism, cell-cycle progression, and growth during stress. Further, kinase inference during DTT suggested new functions for the HOG and PKA pathways in augmenting the unfolded protein response (UPR). Together, our work shows how a high-quality computational network model can facilitate discovery of new pathway interactions during diverse stress responses.
Investigating Signaling Pathway Integration In Saccharomyces Cerevisiae On An Alternative Carbon Source To Coordinate Growth Metabolism And Stress Defense
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Author : Ellen Renee Wagner
language : en
Publisher:
Release Date : 2023
Investigating Signaling Pathway Integration In Saccharomyces Cerevisiae On An Alternative Carbon Source To Coordinate Growth Metabolism And Stress Defense written by Ellen Renee Wagner and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023 with categories.
Due to its relative ease, microbial engineering is invaluable for applied research focused on product formation, particularly for biofuel production. The budding yeast Saccharomyces cerevisiae is an ideal organism for biofuel-based engineering due to its genetic tractability, well researched biology, and preference for fermentation. Even with these advantages, two large bottlenecks for sustainable biofuel production remain. First, when lignocellulosic biomass is broken down, it releases several sugars, the majority being glucose and xylose. While many microorganisms, including yeast, can readily ferment glucose, they lack the ability to ferment the pentose sugar xylose. Second, the process of breaking down lignocellulosic material introduces toxic chemicals into the resulting hydrolysate. These toxins inhibit microbial growth and metabolism, specifically limiting pentose utilization in engineered strains. Through collaborative efforts, we identified loss-of-function mutations in the stress-responsive MAP kinase HOG1 and negative regulator of the RAS/Protein Kinase A (PKA) pathway, IRA2, among other minimal genetic changes, enhances anaerobic xylose fermentation. However, these mutations likely reduce cells' ability to tolerate the toxins present in lignocellulosic hydrolysate, making the strain especially vulnerable to it. As these mutations impact broadly acting signaling networks, the physiological changes required for robust xylose fermentation are unclear. Previously, we generated a strain capable of rapid xylose fermentation with minimal growth by deleting the PKA regulatory subunit BCY1 in the presence of wildtype IRA2 and HOG1. Past work found these strains co-activate the alternative carbon source Snf1 pathway with the PKA pathway to enable xylose utilization. This present a unique model in which to study the integration of three highly conserved signaling pathways for the utilization of a non-native carbon source in the presence of environmental stressors. In chapter 2, we test the contributions of Hog1 and PKA signaling via IRA2 or BCY1 to metabolism, growth, and stress tolerance in mixed sugar media. In chapter 3, we use a multi-omics approach to develop models for how cells coordinate growth, metabolism, and other responses in budding yeast and how restructuring these processes enables anaerobic xylose utilization.
Genome Research
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Author :
language : en
Publisher:
Release Date : 2007
Genome Research written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007 with DNA polymerases categories.
Biotechnology In Japan
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Author :
language : en
Publisher:
Release Date : 1988
Biotechnology In Japan written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1988 with categories.
Yeast Stress Responses
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Author : Stefan Hohmann
language : en
Publisher: Springer Science & Business Media
Release Date : 2007-10-23
Yeast Stress Responses written by Stefan Hohmann and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-10-23 with Science categories.
Every cell has developed mechanisms to respond to changes in its environment and to adapt its growth and metabolism to unfavorable conditions. The unicellular eukaryote yeast has long proven as a particularly useful model system for the analysis of cellular stress responses, and the completion of the yeast genome sequence has only added to its power This volume comprehensively reviews both the basic features of the yeast genral stress response and the specific adapations to different stress types (nutrient depletion, osmotic and heat shock as well as salt and oxidative stress). It includes the latest findings in the field and discusses the implications for the analysis of stress response mechanisms in higher eukaryotes as well.
Stress Activated Protein Kinases
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Author : Francesc Posas
language : en
Publisher: Springer Science & Business Media
Release Date : 2008-01-24
Stress Activated Protein Kinases written by Francesc Posas and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-01-24 with Science categories.
In this book leading researchers in the field discuss the state-of-the-art of many aspects of SAPK signaling in various systems from yeast to mammals. These include various chapters on regulatory mechanisms as well as the contribution of the SAPK signaling pathways to processes such as gene expression, metabolism, cell cycle regulation, immune responses and tumorigenesis. Written by international experts, the book will appeal to cell biologists and biochemists.
Systems Metabolic Engineering
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Author : Hal S. Alper
language : en
Publisher: Humana Press
Release Date : 2013-02-16
Systems Metabolic Engineering written by Hal S. Alper and has been published by Humana Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-02-16 with Science categories.
With the ultimate goal of systematically and robustly defining the specific perturbations necessary to alter a cellular phenotype, systems metabolic engineering has the potential to lead to a complete cell model capable of simulating cell and metabolic function as well as predicting phenotypic response to changes in media, gene knockouts/overexpressions, or the incorporation of heterologous pathways. In Systems Metabolic Engineering: Methods and Protocols, experts in the field describe the methodologies and approaches in the area of systems metabolic engineering and provide a step-by-step guide for their implementation. Four major tenants of this approach are addressed, including modeling and simulation, multiplexed genome engineering, ‘omics technologies, and large data-set incorporation and synthesis, all elucidated through the use of model host organisms. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions on their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, Systems Metabolic Engineering: Methods and Protocols serves as an ideal guide for metabolic engineers, molecular biologists, and microbiologists aiming to implement the most recent approaches available in the field.
Ras Family Gtpases
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Author : Channing Der
language : en
Publisher: Springer
Release Date : 2006-09-13
Ras Family Gtpases written by Channing Der and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006-09-13 with Medical categories.
Since 1982, Ras proteins have been the subject of intense research investigation by the biomedical research community. The wide interest in Ras has been stimulated for three key reasons. This book features chapters contributed by leading investigators in the field that highlight the current state-of-the art in Ras biochemistry, structure and biology. This book is an excellent reference for students in the biomedical sciences and for investigators in the field.
Index Medicus
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Author :
language : en
Publisher:
Release Date : 2004
Index Medicus written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004 with Medicine categories.
Molecular Aspects Of The Stress Response Chaperones Membranes And Networks
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Author : Peter Csermely
language : en
Publisher: Springer Science & Business Media
Release Date : 2007-08-09
Molecular Aspects Of The Stress Response Chaperones Membranes And Networks written by Peter Csermely and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-08-09 with Science categories.
This book makes a novel synthesis of the molecular aspects of the stress response and long term adaptation processes with the system biology approach of biological networks. Authored by an exciting mixture of top experts and young rising stars, it provides a comprehensive summary of the field and identifies future trends.