Regulation of Nitrate and Nitrite Respiration in γ-Proteobacteria: A Comparative Genomics Study

Ravcheev, Dmitry A.; Rakhmaninova, A. B.; Mironov, Andrey A.; Gelfand, Mikhail S.

doi:10.1007/s11008-005-0088-7

Cited by 6 publications

(14 citation statements)

References 48 publications

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“…In comparison with previous studies, where single regulatory systems had been studied in several gamma-protoeobacterial genomes [24,27,33], here we predicted additional regulatory interactions. These predictions were made possible by the use of total pairwise comparison and detailed simultaneous analysis of multiple regulatory systems.…”

Section: Resultssupporting

confidence: 56%

“…It is not surprising, given that in these bacteria the nitrate- and nitrite-respiration system is strongly reduced, and only nitrate, but not nitrite, is used as an electron acceptor [24]. Accordingly, in these organisms, the nitrate respiration plays a less prominent role, and the nitrate-sensing system also is less important as compared to other studied genomes.…”

Section: Discussionmentioning

confidence: 99%

“…So, in most gamma-proteobacteria the fine tuning of the system is not required and a single NarQ-NarP system is sufficient for the control of the nitrate and nitrite respiration [24]. …”

Section: Introductionmentioning

confidence: 99%

“…Previously, comparative genomic analyses were performed separately for Fnr [27], ArcA [28], and NarP [24] in a small number of microorganisms. Here we report the results of a comparative genomic analysis of the respiration regulation in multiple genomes belonging to several representatives of the three families of gamma-proteobacteria.…”

Section: Introductionmentioning

confidence: 99%

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Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae)

et al. 2007

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Background: Gamma-proteobacteria, such as Escherichia coli, can use a variety of respiratory substrates employing numerous aerobic and anaerobic respiratory systems controlled by multiple transcription regulators. Thus, in E. coli, global control of respiration is mediated by four transcription factors, Fnr, ArcA, NarL and NarP. However, in other Gamma-proteobacteria the composition of global respiration regulators may be different.

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Section: Resultssupporting

confidence: 56%

Section: Discussionmentioning

confidence: 99%

“…So, in most gamma-proteobacteria the fine tuning of the system is not required and a single NarQ-NarP system is sufficient for the control of the nitrate and nitrite respiration [24]. …”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae)

et al. 2007

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“…Chemolithoautotrophic nitrate reduction was also demonstrated to be an important process for anaerobic or microaerophilic chemolithoautotrophic bacteria, which were identified as Gammaproteobacteria [33]. The presence of a much more diverse denitrifying community was demonstrated by isolates from a cultivation-dependent research on activated sludge, which included Betaproteobacteria, Alphaproteobacteria, Gammaproteobacteria, Epsilonproteobacteria, Firmicutes and Bacteroidetes [34]. To date, NarX and NarQ genes are confined to species classified in the Gamma and Beta subdivisions of the proteobacteria [27].…”

Section: Electricity Production and Microbial Activitymentioning

confidence: 99%

Microbial community dynamics and electron transfer of a biocathode in microbial fuel cells

Chen

Choi

Cha

et al. 2010

Korean J. Chem. Eng.

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Microbial community dynamics and its electron transfer process within a biocathode in a microbial fuel cell (MFC) were investigated in this study. The MFC was operated steadily over 400 days, and the power density reached 1.92 and 10.27 W/m 3 based on the reduction of nitrate and oxygen, respectively. The six major groups of the clones that were categorized among the 26 clone types were Proteobacteria, Bacteroidetes, Actinobacteria, Planctomycetes, Firmicutes and uncultured bacteria. Microbial community dynamics showed that Betaproteobacteria was replaced by Gammaproteobacteria as the most abundant division among all the clone types with a percentage of 48.86% in the cathode compartment, followed by 20.45% of uncultured bacteria, 17.05% of Bacteroidetes, and others. Distinct oxidation and reduction peaks could be observed in the profiles of cathodic effluent during the cyclic and differential pulse voltammetry tests. It confirmed that nitrate and oxygen reduction in the cathode compartment could be significantly enhanced by the presence of microbes, which are able to excrete metabolites to assist the electron transfer process either in the anode or in the cathode compartment.

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Comparative Genomic Reconstruction of Transcriptional Regulatory Networks in Bacteria

2007

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TFs and their TFBSs (Section 3). Finally, I discuss the likely evolutionary scenarios for bacterial regulons and the balance of conservation and flexibility in the composition of TRNs among species (Section 4). 2. Computational Methods for Identification of Regulatory Motifs 2.1. Structure, Function, and Representation of Transcription Factor Binding Sites 2.1.1. Position of TFBSs in Promoter Regions-TFs regulate gene expression via specific binding to DNA sequences (or operators) located in promoter regions. The DNAbinding affinity and activity of TFs could be modulated by various signals including interaction with small ligands or covalent modification (e.g., phosphorylation by a specific sensor kinase). When a TF binds to an operator, it can either activate or repress transcription initiation. 30 In bacteria, there are TFs that act solely as repressors or as activators, whereas some other TFs have a dual regulatory role in gene expression. Positive or negative effects of such dual TFs depend on the position of the operator site within the target promoter region. Most repressor sites are located between −60 and +60 relative to the transcriptional start site, suggesting that repression by steric hindrance of RNA polymerase binding to the promoter is the most common regulatory mechanism. 31-33 Alternatively, repressors may act by blocking transcription elongation or by looping DNA in the promoter region (Fig. 1). The degree of repression depends significantly on the operator site position relative to the promoter. 34 Analysis of the data for various negatively acting regulators shows large variability in the relative positions of operators and promoters for each regulon. This variation in the repressor site position is in contrast to the relatively fixed positions of activator sites. Activators promote gene expression by binding to an operator that is located either upstream of or adjacent to, the promoter −35 element and by recruiting RNA polymerase to the promoter by direct proteinprotein interaction (Fig. 1). For example, the global catabolic activator Crp in E. coli binds operators, which have a preference to be centered at positions −62.5, −72.5, or −92.5 at Class I promoters, or at position −41.5 at Class II promoters. 35 Some activators (e.g., those from the MerR family) bind at or near to the promoter elements and alter the conformation of the promoter to allow its interaction with RNA polymerase. 30 2.1.2. Structure of TFBSs-The size of a single TFBS usually varies between ~ 12 to 30 nt, the most common length being 16-20 nt. Since TF proteins often recognize and bind to DNA as homodimers or homo-multimeric protein complexes, the TFBSs usually possess an intrinsic symmetry. Cooperative binding of transcription factors to DNA plays an important role in regulating gene expression, ensuring a sigmoid response to the concentration of effector. Inverted repeats (palindromes) and direct repeats are the most common structures of TFBSs. Some homo-multimeric TFs cooperatively bind more complex TFBSs composed of b...

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Regulation of Nitrate and Nitrite Respiration in γ-Proteobacteria: A Comparative Genomics Study

Cited by 6 publications

References 48 publications

Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae)

Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae)

Microbial community dynamics and electron transfer of a biocathode in microbial fuel cells

Comparative Genomic Reconstruction of Transcriptional Regulatory Networks in Bacteria

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