Proteomic Applications in Biology Part 1 docx

Dyer Chapter 2 Fruit Proteomics 33 Ariel Orellana and Ricardo Nilo Chapter 3 Understanding the Pathogenesis of Cytopathic and Noncytopathic Bovine Viral Diarrhea Virus Infection Using

PROTEOMIC APPLICATIONS

IN BIOLOGY Edited by Joshua L Heazlewood

and Christopher J Petzold

Proteomic Applications in Biology

Edited by Joshua L Heazlewood and Christopher J Petzold

Subject Editors: Tsz-Kwong Man and Ricardo J Flores

Published by InTech

Janeza Trdine 9, 51000 Rijeka, Croatia

Copyright © 2011 InTech

All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work Any republication, referencing or personal use of the work must explicitly identify the original source

As for readers, this license allows users to download, copy and build upon published chapters even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications

Notice

Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher No responsibility is accepted for the accuracy of information contained in the published chapters The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book

Publishing Process Manager Martina Durovic

Technical Editor Teodora Smiljanic

Cover Designer InTech Design Team

Image Copyright Photographer - Yves Verhertbruggen

First published January, 2012

Printed in Croatia

A free online edition of this book is available at www.intechopen.com

Additional hard copies can be obtained from orders@intechweb.org

Proteomic Applications in Biology, Edited by Joshua L Heazlewood and

Christopher J Petzold; Subject Editors: Tsz-Kwong Man and Ricardo J Flores

p cm

ISBN 978-953-307-613-3

free online editions of InTech

Books and Journals can be found at

www.intechopen.com

Contents

Preface IX Part 1 Addressing Issues in Agriculture 1

Chapter 1 Food Proteomics: Mapping Modifications 3

Stefan Clerens, Jeffrey E Plowman and Jolon M Dyer Chapter 2 Fruit Proteomics 33

Ariel Orellana and Ricardo Nilo Chapter 3 Understanding the Pathogenesis of Cytopathic

and Noncytopathic Bovine Viral Diarrhea Virus Infection Using Proteomics 53

Mais Ammari, Fiona McCarthy, Bindu Nanduri, George Pinchuk and Lesya Pinchuk

Part 2 Studying Environmental Complexities 67

Chapter 4 Proteomics as a Tool for the Characterization

of Microbial Isolates and Complex Communities 69

Florence Arsène-Ploetze, Christine Carapito, Frédéric Plewniak and Philippe N Bertin Chapter 5 Life in the Cold: Proteomics of

the Antarctic Bacterium Pseudoalteromonas haloplanktis 93

Florence Piette, Caroline Struvay, Amandine Godin, Alexandre Cipolla and Georges Feller

Part 3 Diverse Impacts in Plant Proteomics 115

Chapter 6 Plant Protein Analysis 117

Alessio Malcevschi and Nelson Marmiroli Chapter 7 Assessment of Proteomics Strategies for Plant Cell Wall

Glycosyltransferases in Wheat, a Non-Model Species:

Glucurono(Arabino)Xylan as a Case Study 143

Faik Ahmed

VI Contents

Chapter 8 The Current State of the Golgi Proteomes 167

Harriet T Parsons, Jun Ito, Eunsook Park, Andrew W Carroll, Hiren J Joshi, Christopher J Petzold, Georgia Drakakaki and Joshua L Heazlewood

Part 4 Comparative Approaches in Biology 189

Chapter 9 Differentiation of Four Tuna Species by Two-Dimensional

Electrophoresis and Mass Spectrometric Analysis 191

Tiziana Pepe, Marina Ceruso, Andrea Carpentieri, Iole Ventrone, Angela Amoresano, Aniello Anastasioand Maria Luisa Cortesi Chapter 10 Identification of Proteins Involved in pH Adaptation

in Extremophile Yeast Yarrowia lipolytica 209

Ekaterina Epova, Marina Guseva, Leonid Kovalyov, Elena Isakova, Yulia Deryabina, Alla Belyakova, Marina Zylkova and Alexei Shevelev

Chapter 11 The Role of Conventional Two-Dimensional

Electrophoresis (2DE) and Its Newer Applications in the Study of Snake Venoms 225

Jaya Vejayan, Mei San Tang and Ibrahim Halijah Chapter 12 Protein Homologous to Human CHD1, Which Interacts

with Active Chromatin (HMTase) from Onion Plants 253

DongYun Hyun and Hong-Yul Seo

Preface

In the past decade the field of proteomics has expanded from a highly technical endeavor requiring dedicated practitioners to being widely utilized by researchers of diverse backgrounds for solving complex problems in biology The approach is used broadly to complement basic molecular and biochemical research and encompasses basic protein identification, functional characterization, comparative approaches and

large-scale analyses During this period, technical improvements (e.g., increased

sensitivity, speed, mass accuracy, dynamic range) in mass spectrometric instrumentation provided a solid foundation for proteomic applications outlined in this collection

This book is divided into four sections and is an interesting overview of the diversity and breadth of proteomic applications in biology This is highlighted by the wide range of plant, animal and microbial species that are presented throughout the contents of this volume Especially interesting are the variety of proteomic methods and analytical strategies employed by biological researchers The technical side of proteomics has witnessed enormous changes in sample analysis strategies with many advanced users adopting ‘shotgun’ approaches for protein identification and quantification In contrast, many of the studies outlined in this book employ established, but still powerful, two-dimensional gel electrophoresis strategies to array samples prior to protein identification and/or quantification The advantages of such a visual media for assessment prior to identification are that they are useful and productive when access to high-end mass spectrometers is limited

The first section of this book outlines the utilization of proteomics to address issues in agriculture The increased pressure on food production in the coming decades due to expanding populations and the effects of climate change will require major re-assessments of how food is produced It is extremely likely that proteomic approaches

in combination with other analysis techniques will play an important role in the adaptation of this industry through agricultural research The chapters outlined in this section cover the utilization and application of proteomics to assess the effects of unintended post-translational modifications on food-derived proteins, an overview of approaches and techniques to examine proteins from fruit, and the use of proteomic techniques to understand viral pathogenesis in cattle

X Preface

The second section focuses on the emerging role of metaproteomics to characterize and profile microbes and microbial communities The majority of the Earth’s biomass

is comprised of microorganisms, many of which play essential roles in recycling elements such as carbon and nitrogen While our knowledge of these complex communities is still very limited, recent advances in sequencing technologies, and now proteomics, enable detailed examination of these interesting populations This section provides an overview of current proteomic approaches and methods being used to study microbial communities, demonstrating the utilization of these approaches to characterize a cold tolerant bacterial strain from the Antarctic

The third section addresses the utilization of proteomics to study fundamental processes in plants The development of novel approaches and processes using proteomics can be a direct driver for applications in other areas of biology and applied research This section highlights the specific issues associated with undertaking proteomic analyses in plant biology, demonstrates and assesses its use in understanding the complex process of plant cell wall biosynthesis through a targeted characterization of xylan biosynthesis using multiple approaches by mass spectrometry and finally provides an overview of the subcellular isolation and proteomic characterization of the Golgi apparatus from plants and other species The final section highlights the use of comparative proteomics in biology to understand complex systems One of the most significant contributions to the field of proteomics has been the development of reliable and reproducible quantitation techniques enabling comparative profiling of samples to be undertaken This section examines the use of proteomics to identify protein markers to differentiate commercial tuna species, to identify proteins involved in pH adaptation in yeast strains, the characterization and identification of proteins in snake venom and lastly, the identification and characterization of a protein from onion involved in floral bolting Collectively these chapters outline studies and overviews that employ a wide variety

of proteomic applications in biology These approaches display extensive technical diversity and contrast the use of proteomics from the community level to the individual protein and together highlight the varied ways in which proteomics is being used to expand our understanding of biological systems

Dr Joshua L Heazlewood and Dr Christopher J Petzold

Joint BioEnergy Institute and Physical Biosciences Division

Lawrence Berkeley National Laboratory

Berkeley California,

USA

Part 1

Addressing Issues in Agriculture

1

Food Proteomics: Mapping Modifications

Stefan Clerens1, Jeffrey E Plowman1 and Jolon M Dyer1,2,3

1Food & Bio-Based Products, AgResearch Lincoln Research Centre

2Biomolecular Interaction Centre, University of Canterbury

3Riddet Institute at Massey University, Palmerston North

New Zealand

1 Introduction

Proteins are an essential element in the human diet As food ingredients, they are primarily sourced from plants and animals; important sources include cereals, meat, poultry, fish and dairy Proteomics offers a powerful new way to characterise the protein component of foods Proteomics not only reveals which proteins are expressed in each tissue type, it also allows the investigation of differences in the protein composition of different tissues In addition it has the power to track the proteome of tissues before and after harvest/slaughter, and to evaluate the effect of downstream treatments such as cooking or curing

The proteomic evaluation of food proteins presents a unique set of challenges and opportunities Muscle, milk and cereal proteomes are dominated by very abundant proteins, creating a dynamic range problem In addition to post-translational modifications produced

in vivo, food proteins are subjected to a wide range of post-harvest/post-slaughter

environmental and processing insults prior to consumption These modifications include side-chain oxidation, cross-link formation and backbone cleavage, and critically influence key food properties such as shelf-life, nutritional value, digestibility and health effects

A profound understanding of proteomics, protein modifications and redox chemistry has allowed us to pioneer the application of redox proteomics to foods This has led to the development of a unique proteomics damage scoring system, allowing a direct link between molecular-level understanding to intervention/mitigation at the processing level (Dyer et al., 2010) We anticipate that this ability will be pivotal in the development of next-generation food products

This chapter outlines current achievements in the field of food proteomics It deals with the full spectrum of protein-containing foods, including dairy, meat, seafood and cereal

proteins We focus on ex vivo protein modifications and their effects on foods We devote

attention to redox proteomics approaches applied to food, and pay special attention to the recent development of advanced redox proteomic-based approaches to evaluate and track food protein modifications These approaches are illustrated in a case study that compares the protein damage level in a number of commercially available dairy products

2 Proteins and nutrition

Proteins are key functional and structural components of all living cells and are an essential element in the human diet The human body is capable of synthesising most of the amino

Proteomic Applications in Biology

4

acids from other precursors, but is unable to produce the nine essential amino acids (His, Ile, Leu, Lys, Met, Phe, Thr, Trp, Val), which must be supplied from the diet Another six amino acids (Arg, Cys, Gln, Gly, Pro, Tyr) can be produced by the body, but may need a dietary source when endogenous production cannot meet metabolic requirements Amino acids also act as precursors for many coenzymes, hormones, nucleic acids and other molecules, and can also be used as a metabolic fuel

The total amount of protein in the body is fairly static, but individual proteins are constantly being degraded and re-synthesised The rate of this turnover is affected by stage of life and level of activity That makes the inclusion of an appropriate quantity of high quality protein

in the diet critical for growth and development in children and the maintenance of good health in adults

Protein can be sourced from plants and animals; important sources include cereals, meat, poultry, fish and dairy foods These sources differ in the relative bioavailability of protein and, in particular, essential amino acids In general the digestibility of proteins from vegetable sources is lower than for those of animal origin, being around 78-85% as opposed

to 94-97% for meat, dairy and eggs Animal sources of protein also generally have higher levels of the essential amino acids

Proteomics, through the application of gel and non-gel approaches, offers a powerful new way to characterise the protein component of foods Whereas genomics provides information on the total genome of the organism, proteomics reveals which proteins are actually expressed in each tissue type Furthermore the application of proteomic techniques offers a way to investigate differences in the protein composition of different tissues within

a specific animal or vegetable food type, as well as between different varieties of it In addition it has the power to follow changes in the protein component of various tissues during growth, maturation and post-mortem or post-harvest, as well as downstream treatments such as cooking

3 Food proteomics

This section overviews and summarises the application of classical proteomics in food science, broken down into major food protein groups

3.1 Dairy

Proteomics has been successfully applied to the study of milk proteins by many research teams, and significant effort has gone into the characterisation of the milk proteome Also, bioactive milk components are of enormous scientific and commercial interest Proteomics approaches have been used to compare milk from different species, while proteomic evaluation of other dairy products such as cheese has been a specialist subject that has also received attention

In general, the dynamic range of proteins in milk poses a challenge to proteomics technologies This is because the proteins in milk tend to be dominated by the caseins, which make up some 80% of the total protein content Even when these are removed, the minor components in whey are dominated by one or two proteins; in bovine milk these are α-lactalbumin and β-lactoglobulin Dynamic range issues have been overcome thanks to improvements in mass spectrometer sensitivity, coupled with the application of depletion and/or fractionation techniques Casein, for example, is easily removed by acid precipitation Alternatively affinity purification has been successfully used to remove IgA,