Microbial Proteomics: Development in Technologies and Applications

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 treatmentThis reference work is intended for researchers seeking information on laboratory techniques applied in proteomics research and microbiology. 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