@article {3140,
	title = {Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks.},
	journal = {Nat Commun},
	volume = {4},
	year = {2013},
	month = {2013},
	pages = {1755},
	abstract = {<p>Bacteria contain multiple sigma factors, each targeting diverse, but often overlapping sets of promoters, thereby forming a complex network. The layout and deployment of such a sigma factor network directly impacts global transcriptional regulation and ultimately dictates the phenotype. Here we integrate multi-omic data sets to determine the topology, the operational, and functional states of the sigma factor network in Geobacter sulfurreducens, revealing a unique network topology of interacting sigma factors. Analysis of the operational state of the sigma factor network shows a highly modular structure with σ(N) being the major regulator of energy metabolism. Surprisingly, the functional state of the network during the two most divergent growth conditions is nearly static, with sigma factor binding profiles almost invariant to environmental stimuli. This first comprehensive elucidation of the interplay between different levels of the sigma factor network organization is fundamental to characterize transcriptional regulatory mechanisms in bacteria.</p>},
	keywords = {Energy Metabolism, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Gene Regulatory Networks, Genes, Bacterial, Geobacter, Models, Biological, Regulon, Sigma Factor},
	issn = {2041-1723},
	doi = {10.1038/ncomms2743},
	author = {Qiu, Yu and Nagarajan, Harish and Embree, Mallory and Shieu, Wendy and Abate, Elisa and Ju{\'a}rez, Katy and Cho, Byung-Kwan and Elkins, James G and Nevin, Kelly P and Barrett, Christian L and Lovley, Derek R and Palsson, Bernhard O and Zengler, Karsten}
}
@article {489,
	title = {Computational and experimental analysis of redundancy in the central metabolism of Geobacter sulfurreducens.},
	journal = {PLoS Comput Biol},
	volume = {4},
	year = {2008},
	month = {2008 Feb},
	pages = {e36},
	abstract = {Previous model-based analysis of the metabolic network of Geobacter sulfurreducens suggested the existence of several redundant pathways. Here, we identified eight sets of redundant pathways that included redundancy for the assimilation of acetate, and for the conversion of pyruvate into acetyl-CoA. These equivalent pathways and two other sub-optimal pathways were studied using 5 single-gene deletion mutants in those pathways for the evaluation of the predictive capacity of the model. The growth phenotypes of these mutants were studied under 12 different conditions of electron donor and acceptor availability. The comparison of the model predictions with the resulting experimental phenotypes indicated that pyruvate ferredoxin oxidoreductase is the only activity able to convert pyruvate into acetyl-CoA. However, the results and the modeling showed that the two acetate activation pathways present are not only active, but needed due to the additional role of the acetyl-CoA transferase in the TCA cycle, probably reflecting the adaptation of these bacteria to acetate utilization. In other cases, the data reconciliation suggested additional capacity constraints that were confirmed with biochemical assays. The results demonstrate the need to experimentally verify the activity of key enzymes when developing in silico models of microbial physiology based on sequence-based reconstruction of metabolic networks.},
	keywords = {Bacterial Proteins, Base Sequence, Computer Simulation, Gene Expression Regulation, Bacterial, Geobacter, Models, Biological, Molecular Sequence Data, Multienzyme Complexes, Signal Transduction},
	issn = {1553-7358},
	doi = {10.1371/journal.pcbi.0040036},
	author = {Segura, Daniel and Mahadevan, Radhakrishnan and Ju{\'a}rez, Katy and Lovley, Derek R}
}
