Microbial Proteomics: Development in Technologies and Applications

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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