Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators

Burnham Institute for Medical Research, La Jolla, CA 92037, USA.
Nucleic Acids Research (Impact Factor: 9.11). 05/2008; 36(6):2047-59. DOI: 10.1093/nar/gkn047
Source: PubMed


A novel family of transcription factors responsible for regulation of various aspects of NAD synthesis in a broad range of bacteria was identified by comparative genomics approach. Regulators of this family (here termed NrtR for Nudix-related transcriptional regulators), currently annotated as ADP-ribose pyrophosphatases from the Nudix family, are composed of an N-terminal Nudix-like effector domain and a C-terminal DNA-binding HTH-like domain. NrtR regulons were reconstructed in diverse bacterial genomes by identification and comparative analysis of NrtR-binding sites upstream of genes involved in NAD biosynthetic pathways. The candidate NrtR-binding DNA motifs showed significant variability between microbial lineages, although the common consensus sequence could be traced for most of them. Bioinformatics predictions were experimentally validated by gel mobility shift assays for two NrtR family representatives. ADP-ribose, the product of glycohydrolytic cleavage of NAD, was found to suppress the in vitro binding of NrtR proteins to their DNA target sites. In addition to a major role in the direct regulation of NAD homeostasis, some members of NrtR family appear to have been recruited for the regulation of other metabolic pathways, including sugar pentoses utilization and biogenesis of phosphoribosyl pyrophosphate. This work and the accompanying study of NiaR regulon demonstrate significant variability of regulatory strategies for control of NAD metabolic pathway in bacteria.

Download full-text


Available from: Flavio Cimadamore,
30 Reads
  • Source
    • "Most of the predicted regulators belonged to the protein families whose members were known to regulate pathways for carbohydrate metabolism, such as the AraC, GntR, LacI, and ROK families [46-49]. Two novel regulators for the arabinose and xylose utilization pathways, AraR (BT0354) and XylR (BT0791), belonged to the NrtR family of regulators that were demonstrated to control NAD biosynthesis in other bacterial phyla [50,51]. The experimental characterization of the NrtR-like sugar-responsive regulators in B. thetaiotaomicron is currently underway and will be published elsewhere (D.A. Rodionov, unpublished). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Bacteroides thetaiotaomicron, a predominant member of the human gut microbiota, is characterized by its ability to utilize a wide variety of polysaccharides using the extensive saccharolytic machinery that is controlled by an expanded repertoire of transcription factors (TFs). The availability of genomic sequences for multiple Bacteroides species opens an opportunity for their comparative analysis to enable characterization of their metabolic and regulatory networks. A comparative genomics approach was applied for the reconstruction and functional annotation of the carbohydrate utilization regulatory networks in 11 Bacteroides genomes. Bioinformatics analysis of promoter regions revealed putative DNA-binding motifs and regulons for 31 orthologous TFs in the Bacteroides. Among the analyzed TFs there are 4 SusR-like regulators, 16 AraC-like hybrid two-component systems (HTCSs), and 11 regulators from other families. Novel DNA motifs of HTCSs and SusR-like regulators in the Bacteroides have the common structure of direct repeats with a long spacer between two conserved sites. The inferred regulatory network in B. thetaiotaomicron contains 308 genes encoding polysaccharide and sugar catabolic enzymes, carbohydrate-binding and transport systems, and TFs. The analyzed TFs control pathways for utilization of host and dietary glycans to monosaccharides and their further interconversions to intermediates of the central metabolism. The reconstructed regulatory network allowed us to suggest and refine specific functional assignments for sugar catabolic enzymes and transporters, providing a substantial improvement to the existing metabolic models for B. thetaiotaomicron. The obtained collection of reconstructed TF regulons is available in the RegPrecise database (
    BMC Genomics 12/2013; 14(1):873. DOI:10.1186/1471-2164-14-873 · 3.99 Impact Factor
  • Source
    • "The enzyme from S. oneidensis, which has a two-domain architecture, was also characterized and demonstrated to be functional [7]. This microorganism possesses genes involved in de novo biosynthesis of NAD+ from aspartic acid (via NadA, NadB and NadC, Figure 1), as well as nadV gene coding for the enzyme nicotinamide phosphoribosyltransferase (NadV), which initiates the amidated salvage/recycling of NAM [14]. However, S. oneidensis lacks the genes PncA and PncB (Figure 1), coding for the enzymes supporting conversion of NAM to NaMN via nicotinic acid (NA), which enters the Preiss-Handler pathway that leads to the salvage of NAD+. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Nicotinamide mononucleotide (NMN) deamidase is one of the key enzymes of the bacterial pyridine nucleotide cycle (PNC). It catalyzes the conversion of NMN to nicotinic acid mononucleotide, which is later converted to NAD(+) by entering the Preiss-Handler pathway. However, very few biochemical data are available regarding this enzyme. This paper represents the first complete molecular characterization of a novel NMN deamidase from the halotolerant and alkaliphilic bacterium Oceanobacillus iheyensis (OiPncC). The enzyme was active over a broad pH range, with an optimum at pH 7.4, whilst maintaining 90 % activity at pH 10.0. Surprisingly, the enzyme was quite stable at such basic pH, maintaining 61 % activity after 21 days. As regard temperature, it had an optimum at 65 °C but its stability was better below 50 °C. OiPncC was a Michaelian enzyme towards its only substrate NMN, with a K m value of 0.18 mM and a kcat/K m of 2.1 mM(-1) s(-1). To further our understanding of these enzymes, a complete phylogenetic and structural analysis was carried out taking into account the two Pfam domains usually associated with them (MocF and CinA). This analysis sheds light on the evolution of NMN deamidases, and enables the classification of NMN deamidases into 12 different subgroups, pointing to a novel domain architecture never before described. Using a Logo representation, conserved blocks were determined, providing new insights on the crucial residues involved in the binding and catalysis of both CinA and MocF domains. The analysis of these conserved blocks within new protein sequences could permit the more efficient data curation of incoming NMN deamidases.
    PLoS ONE 12/2013; 8(12):e82705. DOI:10.1371/journal.pone.0082705 · 3.23 Impact Factor
  • Source
    • "The RegPrecise 3.0 contains 40 TF collections (an increase of 31 TFs since the previous database version) that include both widespread TFs such as NrdR, LexA and Zur present in more than 25 diverse taxonomic groups, and narrowly distributed TFs such as Irr in α-proteobacteria and PurR in γ-proteobacteria. Altogether, the orthologous TF collections include 443 regulogs that are valuable for comparative and evolutionary analysis of TF binding motifs and regulon contents, as illustrated by our previous publications on comparative genomics analyses of numerous TFs including HexR [11], Rex [14], NrdR [17], NrtR [30], NiaR [31], KdgR and ExuR [32], AraR and XylR [33], PsrA and LiuR [7], NsrR and NorR [16], Irr and IscR [18], BirA [34], and PaaR [35]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in prokaryotes is one of the critical tasks of modern genomics. Bacteria from different taxonomic groups, whose lifestyles and natural environments are substantially different, possess highly diverged transcriptional regulatory networks. The comparative genomics approaches are useful for in silico reconstruction of bacterial regulons and networks operated by both transcription factors (TFs) and RNA regulatory elements (riboswitches).DescriptionRegPrecise ( is a web resource for collection, visualization and analysis of transcriptional regulons reconstructed by comparative genomics. We significantly expanded a reference collection of manually curated regulons we introduced earlier. RegPrecise 3.0 provides access to inferred regulatory interactions organized by phylogenetic, structural and functional properties. Taxonomy-specific collections include 781 TF regulogs inferred in more than 160 genomes representing 14 taxonomic groups of Bacteria. TF-specific collections include regulogs for a selected subset of 40 TFs reconstructed across more than 30 taxonomic lineages. Novel collections of regulons operated by RNA regulatory elements (riboswitches) include near 400 regulogs inferred in 24 bacterial lineages. RegPrecise 3.0 provides four classifications of the reference regulons implemented as controlled vocabularies: 55 TF protein families; 43 RNA motif families; ~150 biological processes or metabolic pathways; and ~200 effectors or environmental signals. Genome-wide visualization of regulatory networks and metabolic pathways covered by the reference regulons are available for all studied genomes. A separate section of RegPrecise 3.0 contains draft regulatory networks in 640 genomes obtained by an conservative propagation of the reference regulons to closely related genomes. RegPrecise 3.0 gives access to the transcriptional regulons reconstructed in bacterial genomes. Analytical capabilities include exploration of: regulon content, structure and function; TF binding site motifs; conservation and variations in genome-wide regulatory networks across all taxonomic groups of Bacteria. RegPrecise 3.0 was selected as a core resource on transcriptional regulation of the Department of Energy Systems Biology Knowledgebase, an emerging software and data environment designed to enable researchers to collaboratively generate, test and share new hypotheses about gene and protein functions, perform large-scale analyses, and model interactions in microbes, plants, and their communities.
    BMC Genomics 11/2013; 14(1):745. DOI:10.1186/1471-2164-14-745 · 3.99 Impact Factor
Show more

Similar Publications