Genetic characterization and regulation of the nadB locus of Salmonella typhimurium

Structural and Functional Characterization of NadR from Lactococcus lactis

NadR is a bifunctional enzyme that converts nicotinamide riboside (NR) into nicotinamide mononucleotide (NMN), which is then converted into nicotinamide adenine dinucleotide (NAD). Although a crystal structure of the enzyme from the Gram-negative bacterium Haemophilus influenzae is known, structural understanding of its catalytic mechanism remains unclear. Here, we purified the NadR enzyme from Lactococcus lactis and established an assay to determine the combined activity of this bifunctional enzyme. The conversion of NR into NAD showed hyperbolic dependence on the NR concentration, but sigmoidal dependence on the ATP concentration. The apparent cooperativity for ATP may be explained because both reactions catalyzed by the bifunctional enzyme (phosphorylation of NR and adenylation of NMN) require ATP. The conversion of NMN into NAD followed simple Michaelis-Menten kinetics for NMN, but again with the sigmoidal dependence on the ATP concentration. In this case, the apparent cooperativity is unexpected since only a single ATP is used in the NMN adenylyltransferase catalyzed reaction. To determine the possible structural determinants of such cooperativity, we solved the crystal structure of NadR from L. lactis (NadR_Ll). Co-crystallization with NAD, NR, NMN, ATP, and AMP-PNP revealed a ‘sink’ for adenine nucleotides in a location between two domains. This sink could be a regulatory site, or it may facilitate the channeling of substrates between the two domains.

Assimilation of nicotinamide mononucleotide requires periplasmic AphA phosphatase in Salmonella enterica

Salmonella enterica can obtain pyridine from exogenous nicotinamide mononucleotide (NMN) by three routes. In route 1, nicotinamide is removed from NMN in the periplasm and enters the cell as the free base. In route 2, described here, phosphate is removed from NMN in the periplasm by acid phosphatase (AphA), and the produced nicotinamide ribonucleoside (NmR) enters the cell via the PnuC transporter. Internal NmR is then converted back to NMN by the NmR kinase activity of NadR. Route 3 is seen only in pnuC* transporter mutants, which import NMN intact and can therefore grow on lower levels of NMN. Internal NMN produced by either route 2 or route 3 is deamidated to nicotinic acid mononucleotide and converted to NAD by the biosynthetic enzymes NadD and NadE.

Genetic linkage in Pseudomonas aeruginosa of algT and nadB: mutation in nadB does not affect NAD biosynthesis or alginate production

The 68-min region of the chromosome of Pseudomonas aeruginosa (Pa) contains the gene algT, encoding a putative alternate sigma factor similar to sigma E in Escherichia coli, that is required for the expression of several genes in the alginate biosynthetic regulon. Sequences immediately upstream from algT were found to contain a divergently expressed open reading frame encoding a 60-kDa protein with 64 and 36% identity to the nadB gene products of E. coli and Bacillus subtilis, respectively. The nadB gene encodes L-aspartate oxidase and has been shown in several bacteria to be essential for de novo nicotinamide-adenine dinucleotide (NAD) biosynthesis. Pa nadB complemented the growth requirement for nicotinic acid in a nadB mutant strain of E. coli, suggesting that this gene encodes a functional homologue of L-aspartate oxidase. A nadB::Tn501 mutant was constructed by gene replacement in the alginate-producing strain, Pa FRD. This NadB- mutant still produced alginate and appeared normal with respect to the regulation of alginate synthesis. Interestingly, the NadB- mutant did not have an auxotrophic phenotype for nicotinic acid, indicating that this nadB was not essential for NAD biosynthesis in Pa. These results suggest the possibility that Pa has an alternate mechanism for de novo NAD biosynthesis.

The Salmonella typhimurium nadC gene: sequence determination by use of Mud-P22 and purification of quinolinate phosphoribosyltransferase

The Salmonella typhimurium nadC gene and its product, quinolinic acid phosphoribosyltransferase (QAPRTase), were characterized at the molecular and biochemical levels. Fusions of Mud-lac elements isolated in the nadC gene were converted to Mud-P22 insertions. Starting with six original Mud-lac fusions, the entire sequence of the nadC gene was readily obtained. The sequence shows a long open reading frame with two potential initiator methionines, one of which is preceded by the Shine-Dalgarno sequence GGAG-7-nucleotide-ATG. The protein predicted from this second open reading frame is 297 residues in length. The nadC gene was subcloned into a T7-based expression system, allowing for facile purification of the QAPRTase (EC 2.4.2.19) protein to homogeneity. Upon gel filtration, the protein gave an M(r) of 72,000, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis gave a subunit M(r) of 35,000. Automated Edman degradation of several tryptic peptides confirmed the amino acid sequence predicted from the DNA sequence. Chromatography of the apparently homogeneous enzyme on reverse-phase high-performance liquid chromatography resolved two protein species. One of these species failed to give an amino-terminal sequence, while the other yielded the amino-terminal sequence predicted by the second open reading frame and lacked the initiator methionine. The mass of the mature protein, predicted from its DNA sequence, was 32,428 Da. Electrospray mass spectrometry gave masses of 32,501 and 32,581 Da for the two peptides. Steady-state kinetics on the purified QAPRTase indicated Km values of 32 microM for 5-phosphoribosyl-1-pyrophosphate and 20 microM for quinolinate. Vmax was 0.9 U/mg, similar to values reported for this enzyme by other sources.

A genetic characterization of the nadC gene of Salmonella typhimurium

The nadC gene of Salmonella encodes the pyridine biosynthetic enzyme PRPP-quinolinate phosphoribosyltransferase. Using a combination of genetic techniques, a deletion map for the Salmonella nadC gene has been generated which includes over 100 point mutants and 18 deletion intervals. The nadC alleles obtained by hydroxylamine mutagenesis include those suppressed by either amber, ochre, or UGA nonsense suppressors as well as alleles suppressed by the missense suppressor, sumA. Deletions were obtained by three separate protocols including spontaneous selection for loss of the nearby aroP gene, recombination between aroP::MudA and nadC::MudA insertion alleles, and selection for spontaneous loss of tetracycline resistance in a nearby guaC::Tn10dTc insertion mutant allele. The nadC mutants comprise one complementation group and the nadC+ allele is dominant to simple, nadC auxotrophic mutant alleles. Intragenic complementation of two nadC alleles, nadC493 and nadC494, mapping to deletion intervals 17 and 18, respectively, suggests that nadC encodes a multimeric enzyme. Both nadC and the nearby aroP locus are transcribed counterclockwise on the standard genetic map of Salmonella, in opposite orientation to the direction of chromosome replication.

Activity of the nicotinamide mononucleotide transport system is regulated in Salmonella typhimurium

Transport of nicotinamide mononucleotide (NMN) requires two functions, NadI(T) and PnuC. The PnuC protein is membrane associated, as judged by isolation of active TnphoA gene fusions and demonstration that the fusion protein is membrane associated. The PnuC function appears to be the major component of the transport system, since mutant alleles of the pnuC gene permit NMN transport in the absence of NadI(T) function. We present evidence that the activity of the NMN transport system varies in response to internal pyridine levels (presumably NAD). This control mechanism requires NadI(T) function, which is provided by a bifunctional protein encoded by the nadI gene (called nadR by Foster and co-workers [J. W. Foster, Y. K. Park, T. Fenger, and M. P. Spector, J. Bacteriol. 172:4187-4196]). The nadI protein regulates transcription of the nadA and nadB biosynthetic genes and modulates activity of the NMN permease; both regulatory activities respond to the internal pyridine nucleotide level.

The nadI region of Salmonella typhimurium encodes a bifunctional regulatory protein

Mutants of the nadI and pnuA genes were independently isolated on the basis of defects in repression of NAD biosynthetic genes and defects in transport nicotinamide mononucleotide (NMN). The mutations map at min 99 on the Salmonella chromosome, and the affected regions appear to be cotranscribed. Some pairs of nadI and pnuA mutations complement, suggesting the existence of independent functions. However, cis/trans tests with particular mutations provide evidence that both repressor and transport functions are actually performed by a single bifunctional protein. (This result confirms sequencing data of Foster and coworkers [J. W. Foster, Y. K. Park, T. Fenger, and M. P. Spector, J. Bacteriol. 172:4187-4196, 1990]). We have designated the gene for this bifunctional protein nadI and distinguish the regulatory and transport defects with phenotypic designations (R and T). When a nadI(R- T+) mutation (eliminating only repression function) is placed cis to a superrepressor mutation, nadI(Rs T-), the superrepression phenotype is lost. In contrast, placement of R- and Rs T- mutations in trans allows full superrepression. This result suggests that the transport function (eliminated by the Rs T- mutation) and the repression function are provided by the same protein. Insertion mutations in the promoter-proximal repressor region of the nadI gene eliminate transport function unless the inserted element can provide both for both transcription and translation start signals; this finding suggests that there is no transcriptional or translational start between the regions encoding repression and transport functions.

Genetic characterization of the pnuC gene, which encodes a component of the nicotinamide mononucleotide transport system in Salmonella typhimurium

The pnuC gene, which encodes a component of the nicotinamide mononucleotide transport system, has been mapped and oriented. The gene order of the pnuC region, which is at min 17 of the Salmonella chromosome, is nadA-pnuC-aroG-gal. Polarity tests, with pnuC::Mu d-lac operon fusions, reveal that the pnuC gene is the promoter distal gene in an operon with the nadA gene, which encodes the second enzyme of the pyridine biosynthetic pathway. The nadA pnuC operon is regulated by the NadI repressor. The pnuC gene also has its own promoter, since strains with a nadA::Tn10d(Tc) insertion still express the pnuC gene at a low, unregulated level.

Structural gene for NAD synthetase in Salmonella typhimurium

We have identified the structural gene for NAD synthetase, which catalyzes the final metabolic step in NAD biosynthesis. This gene, designated nadE, is located between gdh and nit at 27 min on the Salmonella typhimurium chromosome. Mutants of nadE include those with a temperature-sensitive lethal phenotype; these strains accumulate large internal pools of nicotinic acid adenine dinucleotide, the substrate for NAD synthetase. Native gel electrophoresis experiments suggest that NAD synthetase is a multimeric enzyme of at least two subunits and that subunits from Escherichia coli and S. typhimurium interact to form an active heteromultimer.

Identification of a repressor gene involved in the regulation of NAD de novo biosynthesis in Salmonella typhimurium

Mutations at the nadI locus affect expression of the first two genes of NAD synthesis, nadA and nadB, which are unlinked. Genetic data imply that the regulatory effects of nadI mutations are not due to indirect consequences of physiological alterations. Two types of mutations map in the nadI region. Common null mutations (nadI) show constitutive high-level expression of the nadB and nadA genes. Rare nadIs mutations cause constitutive low-level expression of nadB and nadA. Some nadIs mutations shut off the expression of the biosynthetic genes sufficiently to cause a nicotinic acid auxotrophy. Spontaneous revertants of auxotrophic nadIs mutants have a NadI- phenotype, including some with deletions of the nadI locus. The nadI locus encodes a repressor protein acting on the unlinked nadA and nadB genes.