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See detailRegulation of Bacterial Respiration: Comparison of Microarray and Comparative Genomics Data
Tsyganova, M. O.; Gelfand, M. S.; Ravcheev, Dmitry UL

in Molecular Biology (2007), 41(3), 497-512

A comparison was made of the structures of the Fnr and ArcA modulons and regulons. The data on modulon composition were taken from published microarray assays, whereas regulons were characterized using ... [more ▼]

A comparison was made of the structures of the Fnr and ArcA modulons and regulons. The data on modulon composition were taken from published microarray assays, whereas regulons were characterized using comparative genomic approaches. The regulatory cascade involving Fnr and ArcA contributes greatly to the extension of the Fnr modulon over the Fnr regulon by adding operons of the ArcA modulon. The Fnr and ArcA regulons were shown to contain 26 and 16 operons, respectively. Ten operons had high-score and highly conserved sites for both Fnr and ArcA and were isolated as a so-called core of regulons. [less ▲]

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See detailRegulation of nitrate and nitrite respiration in γ-proteobacteria: a comparative genomics study
Ravcheev, Dmitry UL; Rakhmaninova, A.B.; Mironov, A.A. et al

in Molecular Biology (2005), 39(5), 727-740

Nitrate and nitrite are the most preferable electron acceptors in the absence of molecular oxygen. In the γ-proteobacterium Escherichia coli, nitrate and nitrite respiration is regulated by two homologous ... [more ▼]

Nitrate and nitrite are the most preferable electron acceptors in the absence of molecular oxygen. In the γ-proteobacterium Escherichia coli, nitrate and nitrite respiration is regulated by two homologous tran- scription factors, NarL and NarP. Although this regulatory system was a subject of intensive research for more than 20 years, many key issues, including the structure of the NarL-binding site, are still unclear. Comparative genomics analysis showed that only NarP is responsible for regulation in most γ-proteobacteria. The NarP reg- ulon was studied in ten genomes. Although its structure considerably differs among some genomes, the mech- anism regulating the nitrate and nitrite reduction genes is highly conserved. A correlation was observed between the evolutionary changes in the nitrate and nitrite respiration system and the relevant regulatory system. Poten- tial NarP-binding sites were found upstream of the gene for the global regulator FNR and the sydAB, mdh, and sucAB aerobic metabolism genes. It was assumed on the basis of this evidence that the role of NarP in regulat- ing respiration changed during evolution. In total, 35 new operons were assigned to the generalized NarP reg- ulon. Autoregulation of the narQP operon was suggested for bacteria of the family Vibrionaceae. [less ▲]

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