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By exploring global gene expression of Escherichia coli growing on six different carbon sources, we discovered a striking genome transcription pattern: as carbon substrate quality declines, cells systematically increase the number of genes expressed. Gene induction occurs in a hierarchical manner and includes many factors for uptake and metabolism of better(More)
sigma(32) is the first alternative sigma factor discovered in Escherichia coli and can direct transcription of many genes in response to heat shock stress. To define the physiological role of sigma(32), we have used transcription profiling experiments to identify, on a genome-wide basis, genes under the control of sigma(32) in E. coli by moderate induction(More)
Accepted 9 March, 2006. *For correspondence. E-mail pjkiley @wisc.edu; Tel. ( + 1) 608 262 6632; Fax ( + 1) 608 262 5253. Present address: † The Burnham Institute, La Jolla, CA 92037, USA; ‡ Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA. IscR-dependent gene expression links iron-sulphur cluster assembly to the control(More)
IscR is an iron-sulphur (Fe-S) cluster-containing transcription factor that represses transcription of the operon containing its own gene and the iscSUA-hscBA-fdx genes, whose products are involved in Fe-S cluster biogenesis. In this study, global transcriptional profiling of Escherichia coli IscR(+) and IscR(-) strains grown under aerobic and anaerobic(More)
MOTIVATION A key aspect of elucidating gene regulation in bacterial genomes is identifying the basic units of transcription. We present a method, based on probabilistic language models, that we apply to predict operons, promoters and terminators in the genome of Escherichia coli K-12. Our approach has two key properties: (i) it provides a coherent set of(More)
Bacteria core RNA polymerase (RNAP) must associate with a sigma factor to recognize promoter sequences. Promoters recognized by the sigma(54) (or sigma(N)) associated RNA polymerase are unique in having conserved positions around -24 and -12 nucleotides upstream from the transcriptional start site. Using DNA microarrays representing the entire Escherichia(More)
Bacterial flagellar motility and chemotaxis help cells to reach the most favorable environments and to successfully compete with other micro-organisms in response to external stimuli. Escherichia coli is a motile gram-negative bacterium, and the flagellar regulon in E. coli is controlled by a master regulator FlhDC as well as a second regulator,(More)
The recent availability of heterogeneous high-throughput data types has increased the need for scalable in silico methods with which to integrate data related to the processes of regulation, protein synthesis, and metabolism. A sequence-based framework for modeling transcription and translation in prokaryotes has been established and has been extended to(More)