[Regulation of respiration in enterobacteria: comparison of microarray and comparative genomic data].
Microarrays are widely used for gene expression profiling. In the case of prokaryotes such arrays usually provide data about composition of modulons, groups of genes whose expression is influenced by a single regulatory system or external stimulus. Unlike modulons, regulons include only genes directly controlled by regulatory systems. Here we compared the structures of the Fnr and ArcA modulons and regulons. The data about modulon composition were taken from published microarray assays, whereas regulons were characterized using comparative genomic approaches. The Fnr and ArcA regulons were shown to contain 26 and 16 operons, respectively. Ten operons had high-score and highly conserved site for both Fnr and ArcA. These genes are the "core of regulons". Remarkably, all "core genes" encode enzymes involved in aerobic respiration and central metabolism. The Fnr-ArcA regulatory cascade plays an important role in expansion of the Fnr modulon.
Tsyganova
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Gel'fand
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MS
Ravcheev
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D001425:Bacterial Outer Membrane Proteins / Q000096:biosynthesis / Q000235:genetics; D001426:Bacterial Proteins / Q000096:biosynthesis* / Q000235:genetics; D004734:Energy Metabolism; D004755:Enterobacteriaceae / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000096:biosynthesis / Q000235:genetics; D016680:Genome, Bacterial; D007506:Iron-Sulfur Proteins / Q000096:biosynthesis / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D009876:Operon; D018085:Regulon; D012097:Repressor Proteins / Q000096:biosynthesis / Q000235:genetics
D001425:Bacterial Outer Membrane Proteins; D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; C060704:FNR protein, E coli; D007506:Iron-Sulfur Proteins; D012097:Repressor Proteins; C041610:arcA protein, E coli