Two-component signaling systems. Part C / edited by Melvin I. Simon, Brian R. Crane, Alexandrine Crane. — Amsterdam : Elsevier Academic Press, c2010. – (58.17435/C719/v.471)

Contents

    CONTENTS
    
    Contributors
    Volumes in Series
    1. Characterizing Cross-Talk In Vivo: Avoiding Pitfalls and Overinterpretation
    1. Overview
    2. Sources of Cross-Talk
    3. Cross-Talk Suppression
    4. Transcriptional Reporters
    5. Response Regulator Localization
    6. Phosphatase Cross-Talk
    7. Signal Response in Cross-Talk Networks
    8. Concluding Remarks
    Acknowledgments
    References
    2. Inference of Direct Residue Contacts in Two-Component Signaling
    1. Introduction
    2. Extraction Tools
    3. DCA: Direct Coupling Analysis
    Acknowledgments
    References
    3. Computational Modeling of Phosphotransfer Complexes in Two-Component Signaling
    1. Introduction
    2. Methods
    3. Summary
    Acknowledgments
    References
    4. Kinetic Studies of the Yeast His-Asp Phosphorelay Signaling Pathway
    1. Introduction
    2. Materials and Methods
    3. Conclusion
    Acknowledgments
    References
    5. Purification of MBP-EnvZ Fusion Proteins Using an Automated System
    1. Introduction 78
    2. Comparison Between the Cytoplasmic Domains of E. coli and Typhi EnvZ Proteins
    3. Purification of the Recombinant MBP Proteins by FPLC 82
    4. SDS-PAGE Analysis of Recombinant Expressed MBP-EnvZc Protein 82
    5. Results 84
    6. Discussion 85
    Acknowledgments 85
    References 85
    6. Measurement of Response Regulator Autodephosphorylation Rates Spanning Six Orders of Magnitude 89
    1. Overview of Response Regulator Autodephosphorylation
    2. Purification of Response Regulator Proteins
    3. General Considerations for Autodephosphorylation Assays
    4. Assay of Autodephosphorylation by Loss of 32p
    5. Assay of Autodephosphorylation by Fluorescence
    6. Assay of Autodephosphorylation by Pi Release
    7. Assay of Autodephosphorylation from Systems of Reactions
    8. Future Prospects
    Acknowledgments
    References
    7. Transmembrane Receptor Chimeras to Probe HAMP Domain Function
    1. Introduction
    2. Design of Chimeras of HAMP Domains Fused to the AC Rv3645 Catalytic Domain
    3. Choice of Vector and Cloning Strategy
    4. Expression and Purification of the Chimeras
    5. AC Assay
    6. Example of Applications of the Method and Results
    7. Concluding Remarks
    Acknowledgment
    References
    8. Light-Activated Bacterial LOV-Domain Histidine Kinases 125
    1. Introduction
    2. Description of Method
    3. Concluding Remarks and Future Perspectives
    Acknowledgments
    References
    9. Characterization of Bacteriophytochromes from Photosynthetic Bacteria: Histidine Kinase Signaling Triggered by Light and Redox Sensing
    1. Introduction
    2. Cloning BphP in Expression Vector
    3. Overexpression and Purification of BphPs
    4. Autophosphorylation
    5. Phosphotransfer
    6. Gel Mobility Shift Assay and DNase I Footprint
    7. Gene Disruption
    8. Analysis of the Photosynthetic Phenotypes of the BphP Mutants
    9. Photochemical Measurements
    References
    10. Biophysical Assays for Protein Interactions in the Wsp Sensory System and Biofilm Formation
    1. Introduction
    2. Analyses of the Shape and Molecular Weight of Proteins and Protein Complexes
    3. Experimental Considerations
    4. Case Studies
    5. Concluding Remarks
    Acknowledgments
    References
    11. High-Throughput Screening of Bacterial Protein Localization 185
    1. Introduction
    2. Pipeline Overview
    3. Construction of a Caulobacter ORFeome
    4. Construction of the Fluorescently Tagged Protein Library
    5. Imaging the Caulobacter Protein Localization Library
    6. Image Scoring and Analysis
    7. Conclusion
    Acknowledgments
    References
    12. In vitro and In vivo Analysis of the ArcB/A Redox Signaling Pathway
    1. Introduction
    2， In Vitro Characterization of the Arc TCS
    3. In Vivo Characterization of the Arc TCS
    4. Conclusions
    Acknowledgments
    References
    13. Potassium Sensing Histidine Kinase in Bacillus subtilis
    1. Introduction
    2. Screen for Molecules that Stimulate KinC Sensor Kinase
    3. Quantitative Analysis of the Activation of KinC
    4. Structural Analysis of KinC
    5. Monitoring the Signals Using Indirect Measurements
    6. Applications of the System Signal-Kinase
    7. Conclusions
    References
    14. Two-Component Systems and Regulation of Developmental Progression in Myxococcus xanthus 253
    1. Introduction
    2. Generation of In-Frame Deletions or Point Mutations in the M. xanthus Genome
    3. Phenotype Assays for Analysis of M. xanthus Development
    4. Expression Analysis
    5. In Vitro Biochemical Analysis of TCS Proteins
    Acknowledgment
    References
    15. Two-Component Signaling to the Stress MAP Kinase Cascade in Fission Yeast
    1. Introduction
    2. Detection of Protein Interactions in the H202 Signaling Pathway
    3. Detection of Cysteine S-Thiolation in Tdh1 GAPDH
    Acknowledgments
    References
    16. Genetic and Biochemical Analysis of the SLN1 Pathway in Saccharomyces cerevisiae
    1. Introduction
    2. Materials and Methods
    Acknowledgments
    References
    17. Analysis of Mitogen-Activated Protein Kinase Phosphorylation in Response to Stimulation of Histidine Kinase Signaling Pathways in Neurospora
    1. Introduction
    2. Growth of Cultures and Exposure to Hyperosmotic Conditions or Fungicide
    3. Mitogen-Activated Protein Kinase Assay
    4. Adapting the MAPK Assay
    5. Discussion
    Acknowledgments
    References
    18. Biochemical Characterization of Plant Hormone Cytokinin-Receptor Histidine Kinases Using Microorganisms 335
    1. introduction
    2. Characterization of Plant TCS Components in E. coil
    3. Protocol for Histidine Kinase Assays in E. coil
    4. Protocol of Cytokinin-Binding Assay with Intact E. coil Cells
    5. Preparation of Radioactive Phospho-HPt Factor， and In Vitro Assay of Phosphotransfer to RR
    6. Characterization of Plant TCS Components in S. cerevisiae
    7. Protocol of Histidine Kinase Assay in 5. cerevisiae
    8. Protocol of HPt Factor Assay in 5. cerevisiae
    9. Protocol of Cytokinin-Binding Assay by Using S. pombe Membranes Enriched in AHK4/CRE1
    Acknowledgments
    References
    19. Characterization of Pseudo-Response Regulators in Plants
    1. The Arabidopsis Circadian Clock
    2. Detection of PRR Proteins
    3. Localization of PRR Proteins
    4. Exploring the Circadian Phenotypes of prr Mutants
    5. Concluding Remarks
    Acknowledgments
    References
    20. Reversible Histidine Phosphorylation in Mammalian Cells: A Teeter-Totter Formed by Nucleoside Diphosphate Kinase and Protein Histidine Phosphatase 1
    1. Introduction
    2. Analysis of Phosphorylation and Dephosphorylation of Histidine Residues In Vitro
    3. Functional Analysis of NDPK/PHPT-I Regulated Systems in Living Cells
    References
    21. Histidine Phosphorylation in Histones and in Other Mammalian Proteins
    1. Introduction
    2. Chemical Phosphorylation of Histone H4 Proteins and Peptides
    3. Detection of Phosphohistidine--Phosphoamino Acid Analysis
    4. Filter-Based Assay of Alkali-Stable， Acid-Labile Protein Phosphorylation (Nytran Assay)
    5. In-Gel Kinase Assay
    6. Phosphorylation and Thiophosphorylation Site Analysis by Edman Sequencing
    7. Mass Spectrometric Phosphopeptide Analysis
    Acknowledgments
    References
    Author Index
    Subject Index