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Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts.
Analysis of the genome-wide distribution of the nucleoid-associated protein Fis in Escherichia coli using chromatin immunoprecipitation coupled with high-resolution whole genome-tiling microarrays indicates that A(6)-tracts in particular constitute a high-affinity signal that dictates Fis phasing in stretches of DNA containing multiple and variably spaced A-Tracts and AT-tractions. Expand
Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli
A 4-step method to fully reconstruct the leucine-responsive protein (Lrp) regulon in Escherichia coli K-12 MG 1655 that regulates nitrogen metabolism is presented, elucidating the structure and physiological functions of the Lrp-regulon. Expand
The transcription unit architecture of the Escherichia coli genome
High-throughput, genome-wide measurements of RNA polymerase binding locations and mRNA transcript abundance, 5′ sequences and translation into proteins to determine the organizational structure of the Escherichia coli K-12 MG1655 genome provide an experimentally annotated transcription unit architecture. Expand
Comparative Analysis of Regulatory Elements between Escherichia coli and Klebsiella pneumoniae by Genome-Wide Transcription Start Site Profiling
A new dimension of comparative genomics such that a comparison of two genomes needs to be comprehensive over all levels of genome organization is revealed. Expand
RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media
Analysis of specific small deletions within the rpoC gene encoding the β′-subunit of RNA polymerase (RNAP) suggest that reprogramming the kinetic parameters of RNAP through specific mutations allows regulatory adaptation for optimal growth in new environments. Expand
The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2)
Nucleotide resolution genome-scale measurements of the transcriptome and translatome of Streptomyces coelicolor, the model antibiotic-producing actinomycete, are integrated and it is revealed that the translation efficiency of secondary metabolic genes is negatively correlated with transcription and that several key antibiotic regulatory genes are translationally induced at transition growth phase. Expand
Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states
The reconstructed network of σ-factor and promoter interactions in Escherichia coli reveals the regulatory complexity of the promoter architecture in prokaryotic genomes, and opens a path to the direct determination of the systems biology of their transcriptional regulatory networks. Expand
Cloning and Characterization of a Novel β-Transaminase from Mesorhizobium sp. Strain LUK: a New Biocatalyst for the Synthesis of Enantiomerically Pure β-Amino Acids
The enantioselectivity of the enzyme suggested that the recognition mode of β-aminocarboxylic acids in the active site is reversed relative to that of α-amino acids, which led to the deduced amino acid sequence of the β-transaminase. Expand
Revisit of aminotransferase in the genomic era and its application to biocatalysis
Abstract Aminotransferases (ATs) have useful applications in the chemical industry because of their capability of introducing amino group into ketones or keto acids as well as their highExpand