This volume brings current knowledge of proteomics technologies and related developments with special reference to diseases caused by microbes. The editor has compiled chapters written by expert academicians which distil the information about useful methods in microbial proteomics for the benefit of readers.
Chapters cover several methods used to investigate the microbial proteome and special topics such as antimicrobial drug resistance mechanisms, biomarker developments, post-translational modifications.
Key Features:
- Overview of several biochemical methods in proteomics
- Full-color, high-quality images of the most frequent technologies and applications
- Concise, well organized, and didactic format
- Updates in basic applied information
- Bibliographic references
- Information on proteomics for tuberculosis treatment
This reference work is intended for researchers seeking information on laboratory techniques applied in proteomics research and microbiology.
Table of Contents
Introduction
- The Process of Biofilm Formation
- Attachment
- Micro-Colony Formation
- Detachment
- Mechanism of Biofilm Resistance Against Antimicrobials
- Limited Penetration of Drugs due to Glycocalyx
- Enzyme-Mediated Resistance
- State of Metabolism and Rate of Growth in Biofilms
- Genetic Adaptations
- Efflux Pumps
- Quorum Sensing
- Target Proteins to Study Biofilm
- Proteins Involved in Cellular Metabolism
- Transporter Proteins
- Stress-Responsive Proteins
- Proteomic Techniques to Study Biofilm
- Stable Isotope Labeling by Amino Acids in Cell Culture (Silac)
- Isotope-Coded Affinity Tags (Icat)
- Isobaric Tags for Relative and Absolute Quantification (Itraq)
- Tandem Mass Tags (Tmt)
- Isotope-Coded Protein Label (Icpl)
- Bioorthogonal Noncanonical Amino Acid Tagging (Boncat)
- Future Prospectus
- Conclusion
- Consent for Publication
- Conflict of Interest
- Acknowledgements
- References
- Introduction
- Protein Sample Preparation from Microbial Source
- Clean-Up and Quantification of Proteins
- Gel Electrophoresis of Proteins
Chapter 1 Microbial Biofilm and Drug Resistance: a Proteomic Approach
- Sarika Sharma and Sandeep Sharma
Chapter 2 Past, Present, and Future of Gel-Based Microbial Proteomics
- Munna Lal Yadav, Arvind K. Verma, Preeti Rawat, Abhishek Parashar, Divakar
- Sharma, Sudarshan Kumar and Ashok K. Mohanty
- Types of Page
- Sds-Page (Sodium Dodecyl Sulphate-Polyacrylamide Gel Electrophoresis)
- Tricine Sds-Page
- Native Page
- Sdd-Age (Semi Denaturing Detergent-Agarose Gel Electrophoresis)
- 2D-Page (Two-Dimensional Gel Electrophoresis)
- Isoelectric Focusing (First Dimension)
- Sds-Page (Second Dimension)
- 2D-Dige (Two Dimensional Difference In-Gel Electrophoresis)
- Analysis of 2D Gel and Dige Gel by Different Software
- 2D Gel Analysis Using Image Master 2D Platinum
- Evaluation of Dige Gels Using Decyder
- Comparison Between Ief, Sds-Page, 2D-Page, and Dige
- Microbial Proteomics in Dairy Processing
- Future Perspectives of Gel Based Microbial Proteomics
- Consent for Publication
- Conflict of Interest
- Acknowledgements
- References
- Introduction
- Mass Spectroscopy (Ms)
- Shotgun Ms-Based Proteomics
- Shotgun Ms-Based Quantitative Proteomics
- Experimental Procedure
- I. Sample Preparation
- Ii. Mass Spectrometry
- Data Accomplishment
- Protein Identification
- Use of Maldi-Tof in Microbial Identification and Antimicrobial
- Resistance
- Conclusion
- Consent for Publication
- Conflict of Interest
- Acknowledgements
- References
- Introduction
- Importance of Annotation and Enrichment
- Emerging Trends in Genomics
- Emerging Trends in Proteomics
- Annotation of Microbial Proteins
- Systems Biology and Annotations
- Future Guidelines
- Consent for Publication
- Conflict of Interest
Chapter 3 Liquid Chromatography-Mass Spectrometry (Lcms): An Advanced Tool for the Microbial Proteomics Analysis
- Pranav Kumar Prabhakar
Chapter 4 Functional Annotation and Enrichment of Microbial Proteins Using Systems Biology: Tools and Applications
- Aditya Arya and Vivek Dhar Dwivedi
- Acknowledgements
- References
- Introduction
- What are the General Characteristics of Bacteria and the Significance of the Study?
- What are the Post-Translation Modifications?
- The Biological Significance of Post Translation Modifications and Their Implications
- Ptm Stories Unfolded in Some Pathogenic Organisms
- Role of Ptms in Host-Pathogen Interactions
- Ptm Role in Drug Resistance
- Mechanisms of Bacterial Drug Resistance
- Different Ptms Present in Bacteria
- Acetylation
- Phosphorylation
- Hydroxylation
- Lipidation
- Ampylation
- Adp-Ribosylation
- Glycosylation
- Carboxylation
- Nitrosylation
- Protein Pupylation and Ubiquitin- Like Modifications
- Proteomic Approaches Used in Exploration of Microbial Ptms
- Technical Challenges in the Ptm Which Needs Immediate Attention
- The Lessons Learned from the Past and Giving Way to Future Solutions
- Consent for Publication
- Conflict of Interest
- Acknowledgements
- References
- Introduction
- Bacterial Proteasome: An Evolutionary Precursor of Eukaryotic Proteasome
- Structure - Mycobacterium Proteasome
- Mpa -Mycobacterium Proteasome Atpase
- Pupylation -Mark of Intrinsic Protein Demolition
- Reversed Pupylation -Depupylation
- Recycling of Pup - Proteasome Regulation
- Pup-Proteasome System (Pps) - Bacterial Physiology
- Proteasome - Stress Sensor Machine
- Cpa (Cdc48-Like Protein of Actinobacteria) -A Novel Proteasome Interacting Molecule
- Conclusion and Future Prospects
- Consent for Publication
- Conflict of Interest
- Acknowledgements
- References
Chapter 5 Emerging Paradigm of Post-Translational Modificsations In Microbes: An Undefeatable Weapon
- Arpana Sharma, Chandrajeet Singh, Gopika Raval, Kruti Dave, Ankita Mathur Juhi Sharma and Divakar Sharma
Chapter 6 Pupylation: a Novel Proteolysis Pathway in Prokaryotes
- Yogesh K. Dhuriya and Divakar Sharma
- Introduction
- Overview, Challenges and Probable Solutions
- Enrichment and Extraction of the Complete Proteome from Bacteria
- Protein Precipitation Strategies
- Sds-Tri Chloroacetic Acid (Tca)-Acetone Precipitation for Cell Lysate and Cytosolic
- Proteins
- Acetone Precipitation for Cell Lysate and Cytosolic Proteins
- Ammonium Sulfate Precipitation for Secretory/Culture Filtrate Proteins
- Sds-Tri Chloroacetic Acid (Tca)-Acetone Precipitation for Secretory/Culture Filtrate
- Proteins
- Isolation and Fractionation of Cell Membranes Proteins Through Ultracentrifugation
- Effective Enrichment and Fractionation of Lipophilic Proteins Without Ultracentrifugation 144
- Conclusion and Future Prospects
- Consent for Publication
- Conflict of Interest
- Acknowledgements
- References
- Introduction
- Proteins and Their Role in Infectious Diseases
- Life is the Mode of Action of Proteins - Friedrich Engels
- Techniques Used for Studying Protein-Protein Interactions (Ppi)
- In Silico Methods for Studying Protein-Protein Interactions
- A Note on Biomarkers and Their Role in Infectious Diseases
- Challenges in Studying Protein-Protein Interactions
- Protein Markers in Bacterial and Viral Infections - Pathogen and Host Perspectives
- Influenza
- Hepatitis C
- Dengue
- Human Immunodeficiency Virus -1 (Hiv-1)
- Severe Acute Respiratory Syndrome Coronavirus 2 (Sars-Cov-2)
- Search for Protein Markers in Bacterial Infections - Host and Pathogen Perspectives
- Use of Bacterial Markers for Typing Bacteria
- Determining Antibiotic Resistance
- Proteomics in Biomarker Discovery and Diagnostics
- Biomarkers in Diagnosis, Treatment and Prevention of Infectious Diseases
- The Way Ahead - Future Perspectives
- Consent for Publication
- Conflict of Interest
- Acknowledgements
- References
Chapter 7 Overview and Challenges in Proteins Sample Preparation For 2-Dge in Bacterial Proteomics
- Divakar Sharma, Juhi Sharma, Nirmala Deo and Deepa Bisht
Chapter 8 Proteomics Based Biomarker Development Against Infections: An Overview
- M. Madhan Kumar, Vivek Kumar Gupta and Divakar Sharma
Chapter 9 Microbial Metalloproteome: Approaches and Biomedical Application in Microbial Antibiotics Resistance
- Saroj Sharma, Monalisa Tiwari and Vishvanath Tiwari
- Introduction
- Emergence of Metalloproteomics
- Current Approaches to Metalloproteomics
- Role of Metalloproteins in Microbial Drug Resistance
- Metal Inducible Microbial Proteome and Host-Pathogen
- Interaction
- Targeting Metalloproteins to Target Microbe
- Concluding Remarks and Future Aspects
- Consent for Publication
- Conflict of Interest
- Acknowledgements
- References
- Introduction
- Advancement of Mycobacterial Research Through Proteomics
- Proteomics and Physiology of M. Tuberculosis
- Identification of New Enzymes
- New Substrates
- New Metabolic Pathways
- Proteomics in Developing Novel Biomarkers
- Proteomics and Vaccine Discovery of Mycobacterium
- Tuberculosis
- Pathway of Tb Vaccine Development
- Proteomics and Host-Pathogen Interaction
- Host Cells and Environments for M. Tuberculosis
- Proteomic Analysis of Mycobacterium Tuberculosis-Infected
- Cells
- Proteomics and Structural Biology
- Structure-Based Drug Discovery
- Relationship Between Proteomics and Genomics
- Utility of Proteomics in Drug Discovery
- Conclusion
- Consent for Publication
- Conflict of Interest
- Acknowledgements
- References
- Introduction
- Drug Resistant Tuberculosis
- Clinically Relevant Mtb Proteins
- Antigens of 85 Complex
- Mpt64
- Esat-6 and Cfp-10
- Proteomic Analysis in Mycobacteria
- Sodium Dodecyl Sulphate-Poly Acrylamide Gel Electrophoresis
- Two Dimensional Gel Electrophoresis
Author
- Divakar Sharma
