We propose a new method for inferring S-system models of large-scale genetic networks. The proposed method is based on the problem decomposition strategy and a cooperative coevolutionary algorithm. As the subproblems divided by the problem decomposition strategy are solved simultaneously using the cooperative coevolutionary algorithm, the proposed method can be used to infer any S-system model ready for computational simulation. To verify the effectiveness of the proposed method, we apply it to two artificial genetic network inference problems. Finally, the proposed method is used to analyze the actual DNA microarray data.

The extremely thermophilic bacterium Thermus thermophilus HB8, which belongs to the phylum DeinococcusThermus, has an open reading frame encoding a protein belonging to the cyclic AMP (cAMP) receptor protein (CRP) family present in many bacteria. The protein named T. thermophilus CRP is highly homologous to the CRP family proteins from the phyla Firmicutes, Actinobacteria, and Cyanobacteria, and it forms a homodimer and interacts with cAMP. CRP mRNA and intracellular cAMP were detected in this strain, which did not drastically fluctuate during cultivation in a rich medium. The expression of several genes was altered upon disruption of the T. thermophilus CRP gene. We found six CRP-cAMP-dependent promoters in in vitro transcription assays involving DNA fragments containing the upstream regions of the genes exhibiting de- Cyclic AMP (cAMP) receptor proteins (CRPs) are global transcriptional regulators broadly distributed in bacteria (30,72). The cellular roles of such CRP family proteins are diverse and include carbohydrate metabolism (3, 30), development of competence for transformation (8), modulation of virulence gene expression and pathogenesis (10,11,55,57,65), resuscitation (50), and germination and morphological development (13,49).Escherichia coli CRP controls the activity of over 100 genes and has been the most extensively studied so far (30, 72). This CRP was first named the catabolite gene-activating protein, since it induces the transcription of a number of genes in response to carbon source limitation (16,73). In the absence of a carbon source such as glucose, the intracellular cAMP level increases, resulting in the formation of a CRP-cAMP complex, which binds to specific DNA sequences at target promoters. The CRP-cAMP regulatory complex is also involved in the regulation of genes that are not directly related to catabolism (3). In addition, the complex acts as a negative regulator of transcription at cya gene promoter cyaP2, gal operon promoter galP2, crp gene promoter crpP, and deo operon promoter deoP2 (3). E. coli CRP is a dimer of two identical subunits, each 209 residues in length, and contains a helix-turn-helix DNA-binding motif in its C-terminal domain (40). Each subunit can bind one molecule of allosteric effector cAMP. This CRP undergoes a conformational change upon cAMP binding (21,66,67), and the CRP-cAMP complex interacts with a 22-bp DNA site exhibiting twofold symmetry, with the consensus sequence 5Ј-AAATGTGATCTAGATCACATTT-3Ј (15). Biochemical and genetic analyses have revealed that this CRP interacts with the C-terminal domain of the RNA polymerase (RNAP) ␣ subunit (␣CTD) (5,6,24,35,43,44,58). This interaction is thought to facilitate RNAP binding to the promoter, which leads to the formation of an open complex and induction of transcription initiation. Crystallographic studies on E. coli CRP have been performed to determine the structure of CRP-cAMP and the mechanisms underlying the interactions among CRP-cAMP, DNA, and RNAP ␣CTD (30, 34).CRP homologs have been found not only in othe...

SummaryThermus thermophilus SdrP is one of four cyclic AMP receptor protein (CRP)/fumarate and nitrate reduction regulator (FNR) family proteins from the extremely thermophilic bacterium T. thermophilus HB8. Expression of sdrP mRNA increased in the stationary phase during cultivation at 70°C. Although the sdrP gene was non-essential, an sdrP-deficient strain showed growth defects, particularly when grown in a synthetic medium, and increased sensitivity to disulphide stress. The expression of several genes was altered in the sdrP disruptant. Among them, we found eight SdrP-dependent promoters using in vitro transcription assays. A predicted SdrP binding site similar to that recognized by Escherichia coli CRP was found upstream of each SdrP-dependent promoter. In the wild-type strain, expression of these eight genes tended to increase upon entry into the stationary phase. Transcriptional activation in vitro was independent of any added effector molecule. The hypothesis that apo-SdrP is the active form of the protein was supported by the observation that the three-dimensional structure of apo-SdrP is similar to that of the DNA-binding form of E. coli CRP. Based on the properties of the SdrP-regulated genes found in this study, it is speculated that SdrP is involved in nutrient and energy supply, redox control, and polyadenylation of mRNA.

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