Microbial Proteomics: Development in Technologies and Applications
1st Edition
Published on 31. December 2020
236 pages
978-981-14-9141-2 (ISBN)
Description
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 distill 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.
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Content
- Cover
- Title
- Copyright
- End User License Agreement
- Contents
- Foreword
- Preface
- ACKNOWLEDGEMENTS
- About the Editor
- Dedication
- List of Contributors
- Microbial Biofilm and Drug Resistance: A Proteomic Approach
- Sarika Sharma1 and Sandeep Sharma2,*
- 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
- Past, Present, and Future of Gel-Based Microbial Proteomics
- Munna Lal Yadav1,*, Arvind K. Verma1, Preeti Rawat1, Abhishek Parashar1, Divakar Sharma2, Sudarshan Kumar1 and Ashok K. Mohanty1,*
- INTRODUCTION
- PROTEIN SAMPLE PREPARATION FROM MICROBIAL SOURCE
- CLEAN-UP AND QUANTIFICATION OF PROTEINS
- GEL ELECTROPHORESIS OF PROTEINS
- 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
- Liquid Chromatography-Mass Spectrometry (LCMS): An Advanced Tool for the Microbial Proteomics Analysis
- Pranav Kumar Prabhakar*
- 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
- Functional Annotation and Enrichment of Microbial Proteins Using Systems Biology: Tools and Applications
- Aditya Arya* and Vivek Dhar Dwivedi
- 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
- ACKNOWLEDGEMENTS
- REFERENCES
- Emerging Paradigm of Post-translational Modifications in Microbes: An Undefeatable Weapon
- Arpana Sharma1,2, Chandrajeet Singh1, Gopika Raval2, Kruti Dave2, Ankita Mathur3, Juhi Sharma4 and Divakar Sharma5,*
- 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
- Pupylation: A Novel Proteolysis Pathway in Prokaryotes Functionally Reminiscent to Eukaryotic Ubiquitination
- Yogesh K. Dhuriya1 and Divakar Sharma2,*
- 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
- Overview and Challenges in Proteins Sample Preparation for 2-DGE in Bacterial Proteomics
- Divakar Sharma1 ,*, Juhi Sharma2, Nirmala Deo3 and Deepa Bisht3
- 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
- CONCLUSION AND FUTURE PROSPECTS
- CONSENT FOR PUBLICATION
- CONFLICT OF INTEREST
- ACKNOWLEDGEMENTS
- REFERENCES
- Proteomics Based Biomarker Development Against Infections: An Overview
- M. Madhan Kumar1,*, Vivek Kumar Gupta1 and Divakar Sharma2
- INTRODUCTION
- Proteins and Their Role in Infectious Diseases
- Life is the Mode of Action of Proteins - Friedrich Engels [1]
- 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
- 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
- Proteomics of Mycobacterium Tuberculosis: An Overview
- Anil Kumar Gupta1,3, Divakar Sharma2 and Amit Singh1,3,*
- 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
- Proteome Based Insights in Drug-Resistant Mycobacterium tuberculosis
- Apoorva Narain1, Surya Kant1, Rikesh Kumar Dubey2, Kanchan Srivastava1 and Anand Kumar Maurya3,*
- 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
- Western Blotting
- Enzyme-Linked Immuno Sorbent Assay
- Immunohistochemistry
- Mass Spectrometry
- Isotope-coded Affinity Tag Labeling
- Stable Isotope Labeling by/with Amino Acids in Cell Culture
- Isobaric Tags for Relative and Absolute Quantitation
- X-ray Crystallography
- Nuclear Magnetic Resonance Spectroscopy
- PROSPECTIVE DIRECTION
- CONSENT FOR PUBLICATION
- CONFLICT OF INTEREST
- ACKNOWLEDGEMENTS
- REFERENCES
- Subject Index
