Prokaryotic Systems Biology

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.

Auteur

Nevan Krogan, PhD, is a professor at the UCSF School of Medicine in the Cellular Molecular Pharmacology department. Dr. Krogan's lab focuses on applying global proteomic and genomic approaches to formulate hypotheses about various biological processes, including transcriptional regulation, DNA repair/replication and RNA processing. His lab at UCSF is now developing and applying methodologies to create genetic and physical interactions between pathogenic organisms, including HIV, Mtb, and Dengue, and their hosts, which is providing insight into the human pathways and complexes that are being hijacked during the course of infection.

Mohan Babu, PhD, is an Assistant Professor in the Department of Biochemistry at the University of Regina. Dr. Babu currently holds a CIHR New Investigator award and is a Maud-Menten Finalist of the CIHR Institute of Genetics. He is a member of the Canadian Society of Microbiology, Human Proteome Organization, and Canadian National Proteomics Network. Dr. Babu has developed and applied advanced proteomic, functional genomic, and bioinformatic methods to characterize genome-wide protein and epistatic interaction networks in the budding yeast and gram-negative bacterium, and mammalian cell systems. His group also developed advanced proteomics using affinity purification coupled with mass spectrometry technology to analyze the molecular composition of protein complexes and interactions related to major diseases in humans.

Contenu

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 for 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 ProteinProtein 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 GroEL.- Genetic, Biochemical, and Structural Analyses of Bacterial Surface Polysaccharides.