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Prokaryotic Systems Biology

Part of the Advances in Experimental Medicine and Biology Book Series (volume 883)

Editors: Krogan, PhD, Nevan J.; Babu, PhD, Mohan

DOI: 10.1007/978-3-319-23603-2

ISBN: 978-3-319-23602-5

Publisher: Springer International Publishing - Springer Journals

Aug 7, 2015

1 - 10 of 16 Chapters

LitStream

Chapter 1Metagenomics as a Tool for Enzyme Discovery: Hydrolytic Enzymes from Marine-Related Metagenomes

Popovic, Ana; Tchigvintsev, Anatoly; Tran, Hai; Chernikova, Tatyana N.; Golyshina, Olga V.; Yakimov, Michail M.; Golyshin, Peter N.; Yakunin, Alexander F.

Pages: 1 –20

[This chapter discusses metagenomics and its application for enzyme discovery, with a focus on hydrolytic enzymes from marine metagenomic libraries. With less than one percent of culturable microorganisms in the environment, metagenomics, or the collective study of community genetics, has opened...
LitStream

Chapter 2Investigating Bacterial Protein Synthesis Using Systems Biology Approaches

Gagarinova, Alla; Emili, Andrew

Pages: 21 –40

[Protein synthesis is essential for bacterial growth and survival. Its study in Escherichia coli helped uncover features conserved among bacteria as well as universally. The pattern of discovery and the identification of some of the longest-known components of the protein synthesis machinery,...
LitStream

Chapter 3Biology and Assembly of the Bacterial Envelope

Dufresne, Karine; Paradis-Bleau, Catherine

Pages: 41 –76

[All free-living bacterial cells are delimited and protected by an envelope of high complexity. This physiological barrier is essential for bacterial survival and assures multiple functions. The molecular assembly of the different envelope components into a functional structure represents a...
LitStream

Chapter 4Comparative Genomics and Evolutionary Modularity of Prokaryotes

Bundalovic-Torma, Cedoljub; Parkinson, John

Pages: 77 –96

[The soaring number of high-quality genomic sequences has ushered in the era of post-genomic research where our understanding of organisms has dramatically shifted towards defining the function of genes within their larger biological contexts. As a result, novel high-throughput experimental...
LitStream

Chapter 5Predicting Functional Interactions Among Genes in Prokaryotes by Genomic Context

Moreno-Hagelsieb, G.; Santoyo, G.

Pages: 97 –106

[Genomic context methods for finding functions of unannotated genes were implemented very early after the publication of the first few prokaryotic genomes. The ideas behind these methods include gene fusions, conservation of gene adjacency, and the patters of co-occurrence of genes across...
LitStream

Chapter 6Functional Implications of Domain Organization Within Prokaryotic Rhomboid Proteases

Panigrahi, Rashmi; Lemieux, M. Joanne

Pages: 107 –117

[Intramembrane proteases are membrane embedded enzymes that cleave transmembrane substrates. This interesting class of enzyme and its water mediated substrate cleavage mechanism occurring within the hydrophobic lipid bilayer has drawn the attention of researchers. Rhomboids are a family of...
LitStream

Chapter 7Mapping Transcription Regulatory Networks with ChIP-seq and RNA-seq

Wade, Joseph T.

Pages: 119 –134

[Bacterial genomes encode numerous transcription factors, DNA-binding proteins that regulate transcription initiation. Identifying the regulatory targets of transcription factors is a major challenge of systems biology. Here I describe the use of two genome-scale approaches, ChIP-seq and RNA-seq,...
LitStream

Chapter 8Quantitative and Systems-Based Approaches for Deciphering Bacterial Membrane Interactome and Gene Function

Deineko, Viktor; Kumar, Ashwani; Vlasblom, James; Babu, Mohan

Pages: 135 –154

[High-throughput genomic and proteomic methods provide a concise description of the molecular constituents of a cell, whereas systems biology strives to understand the way these components function as a whole. Recent developments, such as genome editing technologies and protein epitope-tagging...
LitStream

Chapter 9Toward Network Biology in E. coli Cell

Mori, Hirotada; Takeuchi, Rikiya; Otsuka, Yuta; Bowden, Steven; Yokoyama, Katsushi; Muto, Ai; Libourel, Igor; Wanner, Barry L.

Pages: 155 –168

[E. coli has been a critically important model research organism for more than 50 years, particularly in molecular biology. In 1997, the E. coli draft genome sequence was published. Post-genomic techniques and resources were then developed that allowed E. coli to become a model organism for...
LitStream

Chapter 10Genetic Interaction Scoring Procedure for Bacterial Species

Wagih, Omar; Parts, Leopold

Pages: 169 –185

[A genetic interaction occurs when the phenotype of an organism carrying two mutant genes differs from what should have been observed given their independent influence. Such unexpected outcome indicates a mechanistic connection between the perturbed genes, providing a key source of functional...

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