Krogan N. Prokaryotic Systems Biology 2015

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Krogan N. Prokaryotic Systems Biology 2015

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Textbook in PDF format This book focuses on innovative experimental and computational approaches for charting interaction networks in bacterial species. The first part of the volume consists of nine chapters, focusing on biochemical and genetics and genomics approaches including yeast two hybrid, metagenomics, affinity purification in combination with mass spectrometry, chromatin-immunoprecipitation coupled with sequencing, large-scale synthetic genetic screens, and quantitative-based mass spectrometry strategies for mapping the bacterial physical, functional, substrate, and regulatory interaction networks needed for interpreting biological networks, inferring gene function, enzyme discovery, and identifying new drug targets. The second part comprises five chapters, covering the network of participants for protein folding and complex enzyme maturation. It also covers the structural approaches required to understand bacterial intramembrane proteolysis and the structure and function of bacterial proteins involved in surface polysaccharides, outer membrane, and envelope assembly. This volume concludes with a focus on computational and comparative genomics approaches, especially network-based methods for predicting physical or functional interactions, and integrative analytical approaches for generating more reliable information on bacterial gene function. This book provides foundational knowledge in the understanding of prokaryotic systems biology by illuminating how bacterial genes f unction within the framework of global cellular processes. The book will enable the microbiology community to create substantive resources for addressing many pending unanswered questions, and facilitate the development of new technologies that can be applied to other bacterial species lacking experimental data. ​ ​ Front Matter Metagenomics as a Tool for Enzyme Discovery: Hydrolytic Enzymes from Marine-Related Metagenomes Investigating Bacterial Protein Synthesis Using Systems Biology Approaches Biology and Assembly of the Bacterial Envelope Comparative Genomics and Evolutionary Modularity of Prokaryotes Predicting Functional Interactions Among Genes in Prokaryotes by Genomic Context Functional Implications of Domain Organization Within Prokaryotic Rhomboid Proteases Mapping Transcription Regulatory Networks with ChIP-seq and RNA-seq Quantitative and Systems-Based Approaches for Deciphering Bacterial Membrane Interactome and Gene Function Toward Network Biology in E. coli Cell Genetic Interaction Scoring Procedure for Bacterial Species Mapping the Protein–Protein Interactome Networks Using Yeast Two-Hybrid Screens Biogenesis of Escherichia coli DMSO Reductase: A Network of Participants for Protein Folding and Complex Enzyme Maturation Microbial Proteome Profiling and Systems Biology: Applications to Mycobacterium tuberculosis Structural Aspects of Bacterial Outer Membrane Protein Assembly Substrate Interaction Networks of the Escherichia coli Chaperones: Trigger Factor, DnaK and GroE Genetic, Biochemical, and Structural Analyses of Bacterial Surface Polysaccharides Back Matter