dissimilatory metabolism of nitrogen oxides in bacteria comparative reconstruction of transcriptional networks异化的氮氧化物在细菌代谢比较转录网络的重建.pdfVIP

Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks 1,4* 2 3 3 1,4,5 Dmitry A. Rodionov , Inna L. Dubchak , Adam P. Arkin , Eric J. Alm , Mikhail S. Gelfand 1 Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia, 2 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America, 3 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America, 4 State Scientific Center GosNIIGenetika, Moscow, Russia, 5 Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Bacterial response to nitric oxide (NO) is of major importance since NO is an obligatory intermediate of the nitrogen cycle. Transcriptional regulation of the dissimilatory nitric oxides metabolism in bacteria is diverse and involves FNR- like transcription factors HcpR, DNR, and NnrR; two-component systems NarXL and NarQP; NO-responsive activator NorR; and nitrite-sensitive repressor NsrR. Using comparative genomics approaches, we predict DNA-binding motifs for these transcriptional factors and describe corresponding regulons in available bacterial genomes. Within the FNR family of regulators, we observed a correlation of two specificity-determining amino acids and contacting bases in corresponding DNA recognition motif. Highly conserved regulon HcpR for the hybrid cluster protein and some other redox enzymes is present in diverse anaerobic bacteria, including Clostridia, Thermotogales, and delta-proteobacteria. NnrR and DNR control denitrification in alpha- and beta-proteobacteria, respectively. Sigma-54-dependent NorR regulon found in some gamma- and beta-proteobacteria c