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 Anastasio and 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 [...]... crosslinks include lysine, arginine, tyrosine, serine, cysteine and histidine (Taylor and Wang, 2007) Lysine can form a range of crosslinks with other residues (Silvestre et al., 2006) Since lysine is an essential amino acid for nutrition, process-induced lysine crosslinking is of concern in the food industry The best characterised crosslinked modification product is lysinoalanine Lysinoalanine is... morning of slaughter They noted semi-quantitative changes in 27 proteins with muscle ageing, including myosin light chain 1, desmin, troponin T, cofilin 2, F-actin capping protein β subunit, ATP synthase, carbonate dehydrase, triosephosphate isomerise, actin, peroxiredoxin 2, α-b crystalline and heat shock protein 27 kDa Lametsch and Benedixen (2001) used 2-DE to follow post-mortem changes in porcine... by Hunter L*) and drip loss coincided with high proteolysis rates Moreover, 12 proteins appeared to be related to L* values, including αactin, myosin light chain 1, cofilin 2, troponin T and α-b crystalline chaperone proteins In addition four proteins were related to drip values, these being troponin T, adenylate cyclise, ATP-dependent proteinase SP-22 and DJ1 protein Proteomics has also been applied... whey protein concentrate (WPC) and a buttermilk protein concentrate (BPC) using three different approaches Using a LC-MS/MS shotgun proteomics approach, 244 proteins were identified in WPC and 133 in BPC, while label-free profiling was used for semi-quantitative profiling and the determination of protein fingerprints Water soluble extracts of Teleme cheeses prepared from ovine, caprine and bovine milk... proteins are contained within these maps, of which 5092 have been entered into the database Xue et al (2010) applied proteomics to rice with the view to determining its potential for detecting the unintended effects of genetically modified crops By examining the total seed protein expression of two strains of transgenic rice with 2-DE they found that some of the seed proteins in the two lines differed in. .. 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 αlactalbumin and β-lactoglobulin Dynamic range issues have been overcome thanks to improvements in. .. that compensatory growth results in increased post-mortem proteolysis There has been some interest in applying proteomic techniques to analysing cooked pork products, including ham Di Luccia et al (2005) followed the progressive loss by hydrolysis of myofibrillar proteins during the ripening of hams using 2-DE, even to the extent of identifying a novel form of actin in the 2D gel Sentandreu et al (2007)... et al (2010) were also interested in the effects of fish farming on muscle and blood plasma proteomes but this time in changes induced by crowding They found that the proteins mainly affected were those involved in secondary and tertiary stress responses and thus provided insight into the mechanisms causing accelerated muscle pH decline and rigor mortis contraction in salmon living under crowded conditions... and additives and ingredients in processed food, and therefore modifications induced in these proteins during processing and storage and an important consideration for the food as a whole 5 Redox proteomics The emerging proteomic sub-discipline of redox proteomics is based on the study of key reductive and oxidative chemistries occurring within proteins (Dalle-Donne et al., 2006) In complex biological... criteria for ripening at each stage (Kok et al., 2008) Lei et al (2011) developed a legume specific protein database incorporating sequences from seven different legume species which, when applied, resulted in a 54% increase in the average protein score and a 50% increase in the average number of matched peptides When using MALDI-TOF MS data they found their success rate in identifying proteins increased from . ageing, including myosin light chain 1, desmin, troponin T, cofilin 2, F-actin capping protein β subunit, ATP synthase, carbonate dehydrase, triosephosphate isomerise, actin, peroxiredoxin. 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, . loss coincided with high proteolysis rates. Moreover, 12 proteins appeared to be related to L* values, including α- actin, myosin light chain 1, cofilin 2, troponin T and α-b crystalline chaperone