This volume provides a collection of protocols for the common experimental approaches used in the in the burgeoning field of c-di-GMP-dependent signaling. The chapters, divided into eight major parts, guide readers through methods on synthesis, detection, quantitation, modulation of the levels of c-di-GMP present in cells, procedures to detect and evaluate the interaction of c-di-GMP, and up and coming approaches focusing on the inhibition of c-di-GMP signaling.Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to 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.
Authoritative and cutting-edge, c-di-GMP Signaling: Methods and Protocols aims to inspire researchers to try new approaches.
|Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
1. Discovery of the Intracellular Signaling Molecule Cyclic di-GMP
Ute Römling and Michael Y. Galperin
PARt I: Synthesis of c-di-GMP
2. Enzymatic Production of C-di-GMP Using a Thermophilic Diguanylate Cyclase
Prabhadevi Venkataramani and Zhao-Xun Liang
3. Synthesis of [32P]-c-di-GMP for Diguanylate Cyclase and Phosphodiesterase Activity Determinations
Barbara I. Kazmierczak
Part II: Detection and Quantitation of c-di-GMP
4. High-performance Liquid Chromatography (HPLC)-based Detection and Quantitation of Cellular c-di-GMP
Olga E Petrova and Karin Sauer
5. Identification and Quantification of Cyclic Di-Guanosine Monophosphate and its Linear Metabolites by Reversed-Phase LC-MS/MS
Heike Bähre and Volkhard Kaever
6. Detection of Cyclic Dinucleotides by STING
Xiao-Xia Du and Xiao-Dong Su
7. Spectrophotometric and Mass Spectroscopic Methods for the Quantification and Kinetic Evaluation of
In Vitro c-di-GMP Synthesis
Geoffrey B. Severin and Christopher M. Waters
Part III: Visualizing c-di-GMP levels using biosensors
8. Gauging and Visualizing c-di-GMP Levels in Pseudomonas aeruginosa using Fluorescence-based Biosensors
Morten Rybtke, Song Lin Chua, Joey Kuok Hoong Yam, Michael Givskov, Liang Yang, and Tim Tolker-Nielsen
9. Cyclic di-GMP-responsive Tranillegalscriptional Reporter Bioassays in Pseudomonas aeruginosa
Bradley R. Borlee, Grace I. Borlee, Kevin H. Martin, and Yasuhiko Irie
10. Live Flow Cytometry Analysis of c-di-GMP levels in Single Cell Populations
Jongchan Yeo, Xin C. Wang, and Ming C. Hammond
Part IV: Indirect detection of c-di-GMP levels
<
11. Experimental Detection and Visualization of the Extracellular Matrix in Macrocolony Biofilms
Diego O. Serra and Regine Hengge
12. Congo Red Stain Identifies Matrix Overproduction and is an Indirect Measurement for c-di-GMP in many Species of Bacteria
Christopher J. Jones and Daniel J. Wozniak
13. Type IV Pili-dependent Motility as a Tool to Determine the Activity of c-di-GMP Modulating Enzymes in Myxococcus xanthus
Dorota Skotnicka and Lotte Søgaard-Andersen
PART V: Modulation of c-di-GMP levels And bacterial responses
14. Using Light-Activated Enzymes for Modulating Intracellular c-di-GMP Levels in Bacteria
Min-Hyung Ryu, Anastasia Fomicheva, Lindsey O´Neal, Gladys Alexandre, and Mark Gomelsky
15. Analysis of c-di-GMP Levels Synthesized by a Photoreceptor Protein in Response to Different Light Qualities using an in vitro Enzymatic Assay
Veronika Angerer, Lars-Oliver Essen, and Annegret Wilde
16. Probing the Role of Cyclic di-GMP Signalling Systems in Disease using Chinese Radish
Shi-Qi An, Ji-Liang Tang, and J. Maxwell Dow
17. Contribution of Cyclic di-GMP in the Control of Type III and Type VI Secretion in
Pseudomonas aeruginosa Ronan R McCarthy, Martina Valentini, and Alain Filloux
18. Semi-quantitative Analysis of the Red, Dry, and Rough Colony Morphology of Salmonella enterica serovar Typhimurium and Escherichia coli using Congo Red
Annika Cimdins and Roger Simm
Part VI: Measuring c-di-GMP modulating activities
19. Fluorescent 2-aminopurine c-di-GMP and GpG analogs as PDE Probes
Jie Zhou, Clement Opoku-Temeng, and Herman O. Sintim
20. Measuring Cyclic Diguanylate (c-di-GMP)-specific Phosphodiesterase Activity using the MANT-c-di-GMP Assay
Dorit Eli, Trevor E. Randall, Henrik Almblad, Joe J. Harrison, and Ehud Banin
21. Determining Phosphodiesterase Activity (Radioactive Assay)
Barbara I. Kazmierczak
22. Determining Diguanylate Cyclase Activity (Radioactive Assay)
Barbara I. Kazmierczak
PART VII: c-di-GMP binding proteins
23. Detection of c-di-GMP-responsive DNA Binding
Jacob R. Chambers and Karin Sauer
24. Use of Nonradiochemical DNAse Footprinting to Analyze c-di-GMP Modulation of DNA-binding Proteins
Claudine Baraquet and Caroline S. Harwood
25. Detection of Cyclic di-GMP Binding Proteins Utilizing a Biotinylated Cyclic di-GMP Pulldown Assay
Jacob R. Chambers and Karin Sauer
26. Probing Protein-protein Interactions with Genetically Encoded Photo-activatable Crosslinkers
Richard B. Cooley and Holger Sondermann
27. Identification of c-di-AMP-Binding Proteins Using Magnetic Beads
Jan Kampf, Jan Gundlach, Christina Herzberg, Katrin Treffon, and Jörg Stülke
<
28. Pulldown with a c-di-GMP-specific Capture Compound Coupled to Mass Spectrometry as a Powerful Tool to Identify Novel Effector Proteins
Benoît-Joseph Laventie, Timo Glatter, and Urs Jenal
29. Identification of c-di-GMP-responsive Riboswitches
Johann Peltier and Olga Soutourina
30. Isothermal Titration Calorimetry to Determine Apparent Dissociation Constants (Kd) and Stoichiometry of Interaction (n) of c-di-GMP Binding Proteins
Bruno Y. Matsuyama, Petya V. Krasteva, and Marcos V. A. S. Navarro
PART VIII: Targeting c-di-GMP signaling
31. Targeting c-di-GMP Signaling, Biofilm Formation and Bacterial Motility With Small Molecules
Clement Opoku-Temeng and Herman O. Sintim
32. Discovering Selective Diguanylatecyclases Inhibitors: From PleD to Discrimination of the Active Site of cyclic-di-GMP Phosphodiesterases
S. Rinaldo, G. Giardina, F. Mantoni, A. Paiardini, and A. Paone, F. Cutruzzolà
33. High throughput Screening for Compounds that Modulate the Cellular c-di-GMP Level in Bacteria
Julie Groizeleau, Jens Bo Andersen, Michael Givskov, Jens Berthelsen, and Tim Tolker-Nielsen
34. Genetic Tools to Study c-di-GMP-dependent Signaling in Pseudomonas aeruginosa
Livia Leoni, Sarika Vishnu Pawar, and Giordano Rampioni
This volume provides a collection of protocols for the common experimental approaches used in the in the burgeoning field of c-di-GMP-dependent signaling. The chapters, divided into eight major parts, guide readers through methods on synthesis, detection, quantitation, modulation of the levels of c-di-GMP present in cells, procedures to detect and evaluate the interaction of c-di-GMP, and up and coming approaches focusing on the inhibition of c-di-GMP signaling.Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to 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.
Authoritative and cutting-edge, c-di-GMP Signaling: Methods and Protocols aims to inspire researchers to try new approaches.
This volume provides a collection of protocols for the common experimental approaches used in the in the burgeoning field of c-di-GMP-dependent signaling. The chapters, divided into eight major parts, guide readers through methods on synthesis, detection, quantitation, modulation of the levels of c-di-GMP present in cells, procedures to detect and evaluate the interaction of c-di-GMP, and up and coming approaches focusing on the inhibition of c-di-GMP signaling.Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to 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.
Authoritative and cutting-edge, c-di-GMP Signaling: Methods and Protocols aims to inspire researchers to try new approaches.
Discovery of the Intracellular Signaling Molecule Cyclic di-GMP.- Enzymatic Production of C-di-GMP Using a Thermophilic Diguanylate Cyclase.- Synthesis of [
32P]-c-di-GMP for Diguanylate Cyclase and Phosphodiesterase Activity Determinations.- High-performance Liquid Chromatography (HPLC)-based Detection and Quantitation of Cellular c-di-GMP.- Identification and Quantification of Cyclic Di-Guanosine Monophosphate and its Linear Metabolites by Reversed-Phase LC-MS/MS.- Detection of Cyclic Dinucleotides by STING.- Spectrophotometric and Mass Spectroscopic Methods for the Quantification and Kinetic Evaluation of
In Vitro c-di-GMP Synthesis.- Gauging and Visualizing c-di-GMP Levels in
Pseudomonas aeruginosa using Fluorescence-based Biosensors.- Cyclic di-GMP-responsive Tranillegalscriptional Reporter Bioassays in
Pseudomonas aeruginosa .- Live flow cytometry analysis of c-di-GMP levels in Single Cell Populations.- Experimental Detection and Visualization of the Extracellular Matrix in Macrocolony Biofilms.- Congo Red Stain Identifies Matrix Overproduction and is an Indirect Measurement for c-di-GMP in many Species of Bacteria.- Type IV pili-dependent Motility as a Tool to Determine the Activity of c-di-GMP Modulating Enzymes in
Myxococcus xanthus.- Using Light-Activated Enzymes for Modulating Intracellular c di-GMP Levels in Bacteria.- Analysis of c-di-GMP Levels Synthesized by a Photoreceptor Protein in Response to Different Light Qualities using an
in vitro Enzymatic Assay.- Probing the Role of Cyclic di-GMP Signalling Systems in Disease using Chinese Radish.- Contribution of Cyclic di-GMP in the Control of Type III and Type VI Secretion in
Pseudomonas aeruginosa.- Semi-quantitative Analysis of the Red, Dry, and Rough Colony Morphology of
Salmonella enterica serovar Typhimurium
and
Escherichia coli using Congo Red.- Fluorescent 2-aminopurine c-di-GMP and GpG analogs as PDE Probes.- Measuring Cyclic Diguanylate (c-di-GMP)-specific Phosphodiesterase Activity using the MANT-c-di-GMP Assay.- Determining Phosphodiesterase Activity (Radioactive Assay).- Determining Diguanylate Cyclase Activity (Radioactive Assay).- Detection of c-di-GMP-responsive DNA Binding.- Use of Nonradiochemical DNAse Footprinting to Analyze c-di-GMP Modulation of DNA-binding Proteins.- Detection of Cyclic di-GMP Binding Proteins Utilizing a Biotinylated Cyclic di-GMP Pulldown Assay.- Probing Protein-protein Interactions with Genetically Encoded Photo-activatable Crosslinkers.- Identification of c-di-AMP-Binding Proteins Using Magnetic Beads.- Pulldown with a c-di-GMP-specific Capture Compound Coupled to Mass Spectrometry as a Powerful Tool to Identify Novel Effector Proteins.- Identification of c-di-GMP-responsive Riboswitches.- Isothermal Titration Calorimetry to Determine Apparent Dissociation Constants (
Kd) and Stoichiometry of Interaction (
n) of c-di-GMP Binding Proteins.- Targeting c-di-GMP Signaling, Biofilm Formation and Bacterial Motility With Small Molecules.- Discovering Selective Diguanylatecyclases Inhibitors: From PleD to Discrimination of the Active Site of cyclic-di-GMP Phosphodiesterases.- High throughput Screening for Compounds that Modulate the Cellular c-di-GMP Level in Bacteria.- Genetic Tools to Study c-di-GMP-dependent Signaling in
Pseudomonas aeruginosa.
Inhaltsverzeichnis
1. Discovery of the Intracellular Signaling Molecule Cyclic di-GMP Ute Römling and Michael Y. Galperin PARt I: Synthesis of c-di-GMP 2. Enzymatic Production of C-di-GMP Using a Thermophilic Diguanylate Cyclase Prabhadevi Venkataramani and Zhao-Xun Liang 3. Synthesis of [32P]-c-di-GMP for Diguanylate Cyclase and Phosphodiesterase Activity Determinations Barbara I. Kazmierczak Part II: Detection and Quantitation of c-di-GMP 4. High-performance Liquid Chromatography (HPLC)-based Detection and Quantitation of Cellular c-di-GMP Olga E Petrova and Karin Sauer 5. Identification and Quantification of Cyclic Di-Guanosine Monophosphate and its Linear Metabolites by Reversed-Phase LC-MS/MS Heike Bähre and Volkhard Kaever 6. Detection of Cyclic Dinucleotides by STING Xiao-Xia Du and Xiao-Dong Su 7. Spectrophotometric and Mass Spectroscopic Methods for the Quantification and Kinetic Evaluation of In Vitro c-di-GMP Synthesis Geoffrey B. Severin and Christopher M. Waters Part III: Visualizing c-di-GMP levels using biosensors 8. Gauging and Visualizing c-di-GMP Levels in Pseudomonas aeruginosa using Fluorescence-based Biosensors Morten Rybtke, Song Lin Chua, Joey Kuok Hoong Yam, Michael Givskov, Liang Yang, and Tim Tolker-Nielsen 9. Cyclic di-GMP-responsive Tranillegalscriptional Reporter Bioassays in Pseudomonas aeruginosa Bradley R. Borlee, Grace I. Borlee, Kevin H. Martin, and Yasuhiko Irie 10. Live Flow Cytometry Analysis of c-di-GMP levels in Single Cell Populations Jongchan Yeo, Xin C. Wang, and Ming C. Hammond Part IV: Indirect detection of c-di-GMP levels < 11. Experimental Detection and Visualization of the Extracellular Matrix in Macrocolony Biofilms Diego O. Serra and Regine Hengge 12. Congo Red Stain Identifies Matrix Overproduction and is an Indirect Measurement for c-di-GMP in many Species of Bacteria Christopher J. Jones and Daniel J. Wozniak 13. Type IV Pili-dependent Motility as a Tool to Determine the Activity of c-di-GMP Modulating Enzymes in Myxococcus xanthus Dorota Skotnicka and Lotte Søgaard-Andersen PART V: Modulation of c-di-GMP levels And bacterial responses 14. Using Light-Activated Enzymes for Modulating Intracellular c¿di-GMP Levels in Bacteria Min-Hyung Ryu, Anastasia Fomicheva, Lindsey O¿Neal, Gladys Alexandre, and Mark Gomelsky 15. Analysis of c-di-GMP Levels Synthesized by a Photoreceptor Protein in Response to Different Light Qualities using an in vitro Enzymatic Assay Veronika Angerer, Lars-Oliver Essen, and Annegret Wilde 16. Probing the Role of Cyclic di-GMP Signalling Systems in Disease using Chinese Radish Shi-Qi An, Ji-Liang Tang, and J. Maxwell Dow 17. Contribution of Cyclic di-GMP in the Control of Type III and Type VI Secretion in Pseudomonas aeruginosa Ronan R McCarthy, Martina Valentini, and Alain Filloux 18. Semi-quantitative Analysis of the Red, Dry, and Rough Colony Morphology of Salmonella enterica serovar Typhimurium and Escherichia coli using Congo Red Annika Cimdins and Roger Simm Part VI: Measuring c-di-GMP modulating activities 19. Fluorescent 2-aminopurine c-di-GMP and GpG analogs as PDE Probes Jie Zhou, Clement Opoku-Temeng, and Herman O. Sintim 20. Measuring Cyclic Diguanylate (c-di-GMP)-specific Phosphodiesterase Activity using the MANT-c-di-GMP Assay Dorit Eli, Trevor E. Randall, Henrik Almblad, Joe J. Harrison, and Ehud Banin 21. Determining Phosphodiesterase Activity (Radioactive Assay) Barbara I. Kazmierczak 22. Determining Diguanylate Cyclase Activity (Radioactive Assay) Barbara I. Kazmierczak PART VII: c-di-GMP binding proteins 23. Detection of c-di-GMP-responsive DNA Binding Jacob R. Chambers and Karin Sauer 24. Use of Nonradiochemical DNAse Footprinting to Analyze c-di-GMP Modulation of DNA-binding Proteins Claudine Baraquet and Caroline S. Harwood 25. Detection of Cyclic di-GMP Binding Proteins Utilizing a Biotinylated Cyclic di-GMP Pulldown Assay Jacob R. Chambers and Karin Sauer 26. Probing Protein-protein Interactions with Genetically Encoded Photo-activatable Crosslinkers Richard B. Cooley and Holger Sondermann 27. Identification of c-di-AMP-Binding Proteins Using Magnetic Beads Jan Kampf, Jan Gundlach, Christina Herzberg, Katrin Treffon, and Jörg Stülke < 28. Pulldown with a c-di-GMP-specific Capture Compound Coupled to Mass Spectrometry as a Powerful Tool to Identify Novel Effector Proteins Benoît-Joseph Laventie, Timo Glatter, and Urs Jenal 29. Identification of c-di-GMP-responsive Riboswitches Johann Peltier and Olga Soutourina 30. Isothermal Titration Calorimetry to Determine Apparent Dissociation Constants (Kd) and Stoichiometry of Interaction (n) of c-di-GMP Binding Proteins Bruno Y. Matsuyama, Petya V. Krasteva, and Marcos V. A. S. Navarro PART VIII: Targeting c-di-GMP signaling 31. Targeting c-di-GMP Signaling, Biofilm Formation and Bacterial Motility With Small Molecules Clement Opoku-Temeng and Herman O. Sintim 32. Discovering Selective Diguanylatecyclases Inhibitors: From PleD to Discrimination of the Active Site of cyclic-di-GMP Phosphodiesterases S. Rinaldo, G. Giardina, F. Mantoni, A. Paiardini, and A. Paone, F. Cutruzzolà 33. High throughput Screening for Compounds that Modulate the Cellular c-di-GMP Level in Bacteria Julie Groizeleau, Jens Bo Andersen, Michael Givskov, Jens Berthelsen, and Tim Tolker-Nielsen 34. Genetic Tools to Study c-di-GMP-dependent Signaling in Pseudomonas aeruginosa Livia Leoni, Sarika Vishnu Pawar, and Giordano Rampioni
Klappentext
This volume provides a collection of protocols for the common experimental approaches used in the in the burgeoning field of c-di-GMP-dependent signaling. The chapters, divided into eight major parts, guide readers through methods on synthesis, detection, quantitation, modulation of the levels of c-di-GMP present in cells, procedures to detect and evaluate the interaction of c-di-GMP, and up and coming approaches focusing on the inhibition of c-di-GMP signaling.Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to 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.n Authoritative and cutting-edge, c-di-GMP Signaling: Methods and Protocols aims to inspire researchers to try new approaches.
Includes cutting-edge methods and protocols
rn
Provides step-by-step detail essential for reproducible results
rn
Contains key notes and implementation advice from the experts
rn
Includes supplementary material: sn.pub/extras
rn
