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Cover image for Microbial proteomics : functional biology of whole organisms
Title:
Microbial proteomics : functional biology of whole organisms
Series:
Methods of biochemical analysis ; 49
Publication Information:
Hoboken, NJ : Wiley-Liss 2006
ISBN:
9780471699750

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30000010105608 TP248.27.M53 M526 2006 Open Access Book Book
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Summary

Summary

Discover important lessons learned about whole organism biology via microbial proteomics

This text provides an exhaustive analysis and presentation of current research in the field of microbial proteomics, with an emphasis on new developments and applications and future directions in research. The editors and authors show how and why the relative simplicity of microbes has made them attractive targets for extensive experimental manipulation in a quest for both improved disease prevention and treatment and an improved understanding of whole organism functional biology. In particular, the text demonstrates how microbial proteomic analyses can aid in drug discovery, including identification of new targets, novel diagnostic markers, and lead optimization.

Each chapter is written by one or more leading experts in the field and carefully edited to ensure a consistent and thorough approach throughout. Methods, technologies, and tools associated with the most promising approaches are stressed. Key topics covered include:

Microbial pathogenesis at the proteome level Whole cell modeling Structural proteomics and computational analysis Biomolecular interactions Physiological proteomics Metabolic reconstruction using proteomics data

While presenting the practical utility of proteomics data, the text is also clear on the field's current limitations, pointing to areas where further investigation is needed.

Offering a state-of-the-art perspective from internationally recognized experts, this text is ideally suited for researchers and students across the gamut of genomic sciences, including biochemistry, microbiology, molecular biology, genetics, biomedical and pharmaceutical sciences, biotechnology, and veterinary science.


Author Notes

Ian Humphery-Smith, PhD, is the Founding Chair of the Department of Pharmaceutical Proteomics at Utrecht University
Michael Hecker, PhD, is Professor of Microbiology and Head of the Institute for Microbiology at Ernst-Moritz-Arndt-University of Greifswald in Germany


Reviews 1

Choice Review

Proteomics may be roughly described as the study of the regulation of the genome of an organism. Historically, much of the understanding of microbial expression has involved labeling RNA or protein and observing what is expressed. The advantage of proteomics is that one can observe genome expression in the context of the entire genome, not just select genes. Measuring not only the relative level of expression, but also changes in the pattern of protein expression, has become possible. Humphery-Smith (Utrecht Univ.) and Hecker (Ernst-Moritz-Arndt-Univ., Greifswald) offer a compendium that covers the current state of research. The book is divided into 23 chapters, written by experts in their respective areas. Topics range from understanding general metabolic regulation to better understanding pathogenic mechanisms. For example, an understanding of pathogenic mechanisms has historically centered on genes that encode toxins or other virulence factors, often in the absence of a host context. More recent proteomic applications have included the roles of quorum sensing, as well as effects of the host on microbial gene expression in general. The authors have provided a thorough overview of what is still a relatively new field of study. They include large numbers of references. ^BSumming Up: Recommended. Graduate students and above. R. Adler University of Michigan--Dearborn


Table of Contents

Valerie WasingerRobert J. Beynon and Julie M. PrattC. David O'Connor and Ian N. Clarke and Paul SkippRichard Herrmann and Thomas RuppertRicardo Cavicchioli and Amber Goodchild and Mark RafteryLuu Phan-Thanh and Lothar JanschThomas NystromCarol S. GiomettiMary S. Lipton and Margaret F. Romine and Matthew E. Monroe and Dwayne A. Elias and Ljiljana Pasa-Tolic and Gordon A. Anderson and David J. Anderson and Jim Fredrickson and Kim K. Hixson and Christophe Masselon and Heather Mottaz and Nikola Tolic and Richard D. SmithAndreas BurkovskiMogens KilstrupHaike Antelmann and Jan Maarten van Dijl and Sierd Bron and Michael HeckerPhillip CashP. S. Srinivasa Rao and Yuen Peng Tan and Jun Zheng and Ka Yin LeungMichael Strong and Celia W. GouldingCatherine R. Bruce and Pieter van West and Laura J. Grenville-BriggsAida Pitarch and Cesar Nombela and Concha GilAida Pitarch and Cesar Nombela and Concha GilVito G. Delvecchio and Tim Alefantis and Rodolfo A. Ugalde and Diego Comerci and Maria Ines Marchesini and Akbar Khan and Werner Lubitz and Cesar V. MujerGuido GrandiManuela Pruess and Paul Kersey and Tamara Kulikova and Rolf ApweilerBernard Labedan and Olivier LespinetIgor I. Goryanin and Galina V. Lebedeva and Ekaterina A. Mogilevskaya and Eugeniy A. Metelkin and Oleg V. Demin
Prefacep. ix
Acknowledgmentsp. xi
Contributorsp. xiii
Part I General Proteomics of Microorganisms/Model Organismsp. 1
1 Holistic Biology of Microorganisms: Genomics, Transcriptomics, and Proteomicsp. 3
2 Strategies for Measuring Dynamics: The Temporal Component of Proteomicsp. 15
3 Quest for Complete Proteome Coveragep. 27
4 Proteome of Mycoplasma pneumoniaep. 39
5 Proteomics of Archaeap. 57
Part II Proteomics and Cell Physiologyp. 73
6 Elucidation of Mechanisms of Acid Stress in Listeria monocytogenes by Proteomic Analysisp. 75
7 Oxidation of Bacterial Proteome in Response to Starvationp. 89
8 Tale of Two Metal Reducers: Comparative Proteome Analysis of Geobacter sulferreducens PCA and Shewanella oneidensis MR-1p. 97
9 AMT Tag Approach to Proteomic Characterization of Deinococcus radiodurans and Shewanella oneidensisp. 113
Part III Physiological Proteomics of Industrial Bacteriap. 135
10 Proteomics of Corynebacterium glutamicum: Essential Industrial Bacteriump. 137
11 Proteomics of Lactococcus lactis: Phenotypes for a Domestic Bacteriump. 149
12 Proteomic Survey through Secretome of Bacillus subtilisp. 179
Part IV Proteomics of Pathogenic Microorganismsp. 209
13 Analyzing Bacterial Pathogenesis at Level of Proteomep. 211
14 Unraveling Edwardsiella tarda Pathogenesis Using the Proteomics Approachp. 237
15 Structural Proteomics and Computational Analysis of a Deadly Pathogen: Combating Mycobacterium tuberculosis from Multiple Frontsp. 245
16 Proteomic Studies of Plant-Pathogenic Oomycetes and Fungip. 271
17 Candida albicans Biology and Pathogenicity: Insights from Proteomicsp. 285
18 Contributions of Proteomics to Diagnosis, Treatment, and Prevention of Candidiasisp. 331
19 Identification of Protein Candidates for Developing Bacterial Ghost Vaccines against Brucellap. 363
20 Genomics and Proteomics in Reverse Vaccinesp. 379
Part V Proteome Databases, Bioinformatics, and Biochemical Modelingp. 395
21 Databases and Resources for in silico Proteome Analysisp. 397
22 Interspecies and Intraspecies Comparison of Microbial Proteins: Learning about Gene Ancestry, Protein Function, and Species Life Stylep. 415
23 Cellular Kinetic Modeling of the Microbial Metabolismp. 437
Indexp. 489
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