Microbial Proteomics: Development in Technologies and Applications

Divakar Sharma

• Publisher: Bentham Science Publishers
• Year: 2020
• Print ISBN: 9789811491429
• eBook ISBN: 9789811491412
• Topic: Biowissenschaften
• Subtopic: Wissenschaft Geschichte & Praxis

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.

Emerging Paradigm of Post-translational Modifications in Microbes: An Undefeatable Weapon

Arpana Sharma^{1, 2}, Chandrajeet Singh¹, Gopika Raval², Kruti Dave², Ankita Mathur³, Juhi Sharma⁴, Divakar Sharma^{5, *}

¹ Central University of Gujarat, Gandhinagar, India

² Mehsana Urban Institute of Sciences, Department of Biotechnology, Ganpat University, Kherva, 384012, India

³ Mewar University, Gangrar, Chittorgarh, Udaipur, 312901, India

⁴ Department of Botany and Microbiology, St. Aloysius College, Sadar Cantt, Jabalpur, 482002, India

⁵ CRF, Mass Spectrometry Laboratory, Kusuma School of Biological Sciences (KSBS), Indian Institute of Technology, Delhi, 110016, India

Abstract

Bacteria are simple organisms, optimized with basic but robust cell regulation mechanisms for efficient growth. Nonetheless, fitting in the description, they possess remarkable adaptive capacity with diverse survival strategies. Post-translational modifications (PTMs) provide a competitive edge to adapt bacteria with limiting, fluctuating nutrients and extremes of environment variables. PTM is one of the cellular processes in bacteria and helps them to adapt to a new environment for their survival. Several post-translation modifications regulate bacterial functions and provide strength to bacteria for surviving in adverse conditions. On-going investigations revealed many reversible or irreversible novel bacterial PTMs like the addition of simple group (acetylation, phosphorylation, methylation and hydroxylation) or composite molecules (AMPylation, ADP-ribosylation, glycosylation and isoprenylation), or small protein ubiquitin and modifying the side chain residues like (elimination and deamidation). PTMs are recognized as important players in directing cellular dynamics like cell metabolism, stress response, pathogenesis and virulence factors. Bacteria with several PTMs are capable of modulating the signaling pathways by destabilising the host cell defense machinery, protein-protein interactions, ultimately promoting their replication. Currently, many studies focus on the relationship between PTMs and antibiotic resistance, increasing bacterial tolerance to various antimicrobials. A paradoxical behaviour is that a single protein may be modified at one or variable positions in interspecies, but changes also exist in the same species. So, to characterize the multifaceted interactions of PTMs, it is still a challenge in metabolic engineering,

synthetic biology, and medical sciences. Therefore, understanding of bacterial PTMs and PTMs directed host proteins modification will provide better insights into host-pathogen interaction. This chapter focuses on the roles of PTMs in nutrition sequestration and cellular response. Furthermore, we discuss the prospects and advances of proteomics tools in enhancing knowledge related to PTMs of human gut microbiota.

Keywords: Acetylation, Carboxylation, Glycosylation, Interactomics, Lipidation, Methylation, Microbial proteins, Nitrosylation, Phosphorylation, Post-translational modifications, Proteomic tools.

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^* Corresponding author Divakar Sharma: CRF, Mass Spectrometry Laboratory, Kusuma School of Biological Sciences (KSBS), Indian Institute of Technology, Delhi, 110016, India; Tel: [phone]; E-mail: [email protected]

INTRODUCTION

Bacteria are simple, single-celled organisms that can thrive in extreme environmental conditions. They are classified as prokaryotic cells which have a simple internal structure, lack a nucleus and contain DNA in the form of a loosely warped fiber-like structure called “nucleoid”. The relationship of human-bacteria is complicated as some bacteria are useful while others are disease-causing. They have been seen in many associations such as symbiotic, parasitic or commensalism. In the symbiotic associations, natural selection favours the organisms to interact within species in a manner to favour them in extreme environments, which is absent in the individual species. The bacteria, which associate together as co-cultures, which have many advantages in the biotechnology industries, are also a very important part of gut microbiota, which are essential for the normal working of the host organisms [1]. Most of the mutualistic associations are harmless, but there are some which are harmful and cause the disease to the human species. Such bacteria are identified as pathogenic organisms and their symbiotic interactions cause infectious diseases and host damage [2, 3]. These pathogenic microorganisms adapt themselves by immune-compromising the host by suppressing innate immunity to survive in the host cells, subsequently posing a constant challenge to human wellbeing.

Hence, infection biology has been in use over the years to study the abnormal responses which are acquired by the pathogenic organisms inside the host cells. The bacteria have a specific infection cycle, which is identified [4]. Firstly they will introduce into the host tissue by a specific mode of transmission. Subsequently, they will adhere to the tissues and establish themselves by evading the host immune responses. Consequently, they will disseminate into the nearby tissues by secreting toxins. In the process, they will hijack the host molecular mechanisms and mimic the same for its growth.

Nowadays, there is an appearance of many multidrug resistance species, which has created a lot of curiosity in the infection biology fields. Also, with the advancement of proteomic techniques, there is a lot of research going on to study the molecular signals during infections. The assertiveness of virulence and infection is due to the secretion of various proteins that may be secreted in the original form or may be modified [5].

It has been investigated that various post-translational modifications have been studied, which have been shown to increase the virulence and pathogenicity of bacteria. It is pivotal that these protein secretion systems must be studied and understood for the eradication of the pathogens. To curb the bacterial disease, it is important to target any of these proteins and their secretion systems [6].

Bacterial cells change their endogenous biochemical functions to adapt to the altering environmental conditions. They achieve these adjustments by successive post-translational modifications (PTMs), which alter the biological and chemical properties of proteins. Till date, approximately 200 PTMs have been established and illustrated by many novel proteomic approaches. These PTMs are very important as they confer important protein function properties, maintains its stability, modifies its activity to the changing environmental cues and helps in establishing interactions with ...

Table of contents

• Welcome
• Table of Content
• Title
• BENTHAM SCIENCE PUBLISHERS LTD.
• PREFACE
• FOREWORD
• About the Editor
• DEDICATION
• List of Contributors
• Microbial Biofilm and Drug Resistance: A Proteomic Approach
• Past, Present, and Future of Gel-Based Microbial Proteomics
• Liquid Chromatography-Mass Spectrometry (LCMS): An Advanced Tool for the Microbial Proteomics Analysis
• Functional Annotation and Enrichment of Microbial Proteins Using Systems Biology: Tools and Applications
• Emerging Paradigm of Post-translational Modifications in Microbes: An Undefeatable Weapon
• Pupylation: A Novel Proteolysis Pathway in Prokaryotes Functionally Reminiscent to Eukaryotic Ubiquitination
• Overview and Challenges in Proteins Sample Preparation for 2-DGE in Bacterial Proteomics
• Proteomics Based Biomarker Development Against Infections: An Overview
• Microbial Metalloproteome: Approaches and Biomedical Application in Microbial Antibiotics Resistance
• Proteomics of Mycobacterium Tuberculosis: An Overview
• Proteome Based Insights in Drug-Resistant Mycobacterium tuberculosis