The role of the NAC protein in the nitrogen regulation of Klebsiella aerogenes

The NAC (nitrogen assimilation control) protein from Klebsiella aerogenes is a LysR-like regulator for transcription of several operons involved in nitrogen metabolism, and couples the transcription of these sigma 70-dependent operons to regulation by the sigma 54-dependent NTR system. NAC activates expression of operons (e.g. histidine utilization, hut), allowing use of poor nitrogen sources, and represses expression of operons (e.g. glutamate dehydrogenase, gdh) allowing assimilation of the preferred nitrogen source, ammonium. NAC is both necessary and sufficient to activate transcription, but the expression of the nac gene is totally dependent on the central nitrogen regulatory system (NTR) and RNA polymerase carrying the sigma 54 sigma factor (RNAP sigma 54). Nitrogen starvation signals the NTR system to transcribe nac, and NAC activates the transcription of hut, put (proline utilization), and urease. NAC does not affect the transcription of RNAP sigma 54-dependent operons like ginA or nifLA, which respond directly to the NTR system, but activates transcription of RNAP sigma 70-dependent operons. Thus NAC acts as a bridge between RNAP sigma 70-dependent operons like hut and the RNAP sigma 54-dependent NTR system. The activation of operons like hut by NAC in response to nitrogen starvation is at least superficially similar to their activation by CAP-cAMP in response to carbon and energy starvation.

Klebsiella aerogenes catabolite gene activator protein and the gene encoding it (crp)

The catabolite gene activator protein from Klebsiella aerogenes (CAPK) and the corresponding protein from Escherichia coli (CAPE) were shown to be nearly identical. Both CAPK and CAPE activated transcription from the CAP-dependent promoters derived from E. coli and K. aerogenes. The crp gene from K. aerogenes (encoding CAP) is tightly linked to rpsL. The nucleotide sequence of crp predicts an amino acid sequence for CAPK that differs in only one position from that of CAPE.

In vitro transcription of the histidine utilization (hutUH) operon from Klebsiella aerogenes

The promoter region preceding the hutUH operon in Klebsiella aerogenes contains two oppositely oriented, overlapping promoters. In the absence of catabolite gene activator protein-cyclic AMP (CAP-cAMP), transcription proceeds primarily from the backward-oriented promoter (Pc), whose function has not yet been determined, and only very weakly from the forward hutUH promoter, hutUp. In the presence of CAP-cAMP, Pc is repressed and transcription from hutUp is favored. Two protein components required for this in vitro transcription system, RNA polymerase (RNAP) and CAP, were purified from K. aerogenes and were shown to be functionally interchangeable with the corresponding proteins from Escherichia coli, suggesting that E. coli RNAP could be used to study some aspects of hut transcription. We showed that a gradual activation of hutUp (by increasing concentrations of CAP, cAMP, or glycerol) resulted in a parallel repression of Pc, arguing in favor of a direct competition between the two promoters. The presence of a DNA sequence resembling the consensus for CAP-binding sites and centered at nucleotide -82 (relative to hutUp) initially suggested that a primary role of CAP was to repress Pc, thereby indirectly activating hutUp. However, the relatively slow formation of open complexes at Pc, even in the absence of CAP-cAMP, showed that Pc is a weak promoter and likely to be a poor competitor for RNAP. The observed dominance of Pc over hutUp suggested that the latter is an even weaker promoter. Thus, repression of Pc would not be sufficient to cause the observed increase in hutUp activity, and the CAP-cAMP complex must play a direct role in the activation of hutUp.

Regulation of assimilatory nitrate reductase formation in Klebsiella aerogenes W70

Klebsiella aerogenes W70 could grow aerobically with nitrate or nitrite as the sole nitrogen source. The assimilatory nitrate reductase and nitrite reductase responsible for this ability required the presence of either nitrate or nitrite as an inducer, and both enzymes were repressed by ammonia. The repression by ammonia, which required the NTR (nitrogen regulatory) system (A. Macaluso, E. A. Best, and R. A. Bender, J. Bacteriol. 172:7249-7255, 1990), did not act solely at the level of inducer exclusion, since strains in which the expression of assimilatory nitrate reductase and nitrite reductase was was independent of the inducer were also susceptible to repression by ammonia. Insertion mutations in two distinct genes, neither of which affected the NTR system, resulted in the loss of both assimilatory nitrate reductase and nitrite reductase. One of these mutants reverted to the wild type, but the other yielded pseudorevertants at high frequency that were independent of inducer but still responded to ammonia repression.

Cloning of the Klebsiella aerogenes nac gene, which encodes a factor required for nitrogen regulation of the histidine utilization (hut) operons in Salmonella typhimurium

The nac (nitrogen assimilation control) gene from Klebsiella aerogenes, cloned in a low-copy-number cloning vector, restored the ability of K. aerogenes nac mutants to activate histidase and repress glutamate dehydrogenase formation in response to nitrogen limitation and to limit the maximum expression of the nac promoter. When present in Salmonella typhimurium, the K. aerogenes nac gene allowed the hut genes to be activated during nitrogen-limited growth. Thus, the nac gene encodes a cytoplasmic factor required for activation of hut expression in S. typhimurium during nitrogen-limited growth.

Tn1000-mediated insertion mutagenesis of the histidine utilization (hut) gene cluster from Klebsiella aerogenes: genetic analysis of hut and unusual target specificity of Tn1000

The histidine utilization (hut) genes from Klebsiella aerogenes were cloned in both orientations into the HindIII site of plasmid pBR325, and the two resulting plasmids, pCB120 and pCB121, were subjected to mutagenesis with Tn1000. The insertion sites of Tn1000 into pCB121 were evenly distributed throughout the plasmid, but the insertion sites into pCB120 were not. There was a large excess of Tn1000 insertions in the "plus" or gamma delta orientation in a small, ca. 3.5-kilobase region of the plasmid. Genetic analysis of the Tn1000 insertions in pCB120 and pCB121 showed that the hutUH genes form an operon transcribed from hutU and that the hutC gene (encoding the hut-specific repressor) is independently transcribed from its own promoter. The hutIG cluster appears not to form an operon. Curiously, insertions in hutI gave two different phenotypes in complementation tests against hutG504, suggesting either that hutI contains two functionally distinct domains or that there may be another undefined locus within the hut cluster. The set of Tn1000 insertions allowed an assignment of the gene boundaries within the hut cluster, and minicell analysis of the polypeptides expressed from plasmids carrying insertions in the hut genes showed that the hutI, hutG, hutU, and hutH genes encode polypeptides of 43, 33, 57, and 54 kilodaltons, respectively.

Nucleotide sequence of the gene encoding the repressor for the histidine utilization genes of Klebsiella aerogenes

The hutC gene of Klebsiella aerogenes encodes a repressor that regulates expression of the histidine utilization (hut) operons. The DNA sequence of a region known to contain hutC was determined and shown to contain two long rightward-reading open reading frames (ORFs). One of these ORFs was identified as the 3' portion of the hutG gene. The other ORF was the hutC gene. The repressor predicted from the hutC sequence contained a helix-turn-helix motif strongly similar to that seen in other DNA-binding proteins, such as lac repressor and the catabolite gene activator protein. This motif was located in the N-terminal portion of the protein, and this portion of the protein seemed to be sufficient to allow repression of the hutUH operon but insufficient to allow interaction with the inducer. The presence of a promoterlike sequence and a ribosome-binding site immediately upstream of the hutC gene explained the earlier observation that hutC can be transcribed independently of the other hut operon genes. The predicted amino acid sequence of hut repressor strongly resembled that of the corresponding protein from Pseudomonas putida (S. L. Allison and A. T. Phillips, J. Bacteriol. 172:5470-5476, 1990). An unexpected, leftward-reading ORF extending from about the middle of hutC into the preceding (hutG) gene was also detected. The deduced amino acid sequence of this leftward ORF was quite distinct from that of an unexpected ORF of similar size found immediately downstream of the P. putida hutC gene. The nonstandard codon usage of this leftward ORF and the expression of repressor activity from plasmids with deletions in this region made it unlikely that this ORF was necessary for repressor activity.

Cyclophosphamide therapy of idiopathic hepatic granulomatosis

A 50-year-old woman presented with idiopathic hepatic granulomatosis and autoimmune hemolytic anemia. Splenectomy corrected the anemia, and the liver disorder responded to prednisone. However, her liver disease relapsed on four occasions when prednisone was tapered, including three episodes when hepatic granulomatosis was proven by biopsy. Cyclophosphamide therapy allowed prednisone withdrawal, and she has remained in clinical and biochemical remission for two years on a low dose of the drug.

Cell-cycle-dependent polar morphogenesis in Caulobacter crescentus: roles of phospholipid, DNA, and protein syntheses

During swarmer cell differentiation in Caulobacter crescentus, morphogenesis at the swarmer pole is characterized by the loss of the flagellum, by the loss of phage receptor activity (PRA) (the ability of the cell to adsorb phage phi CbK), and finally by the initiation of stalk outgrowth at the site formerly occupied by the flagellum and the PRA. We show here that each of these events is a cell cycle-dependent event requiring continuous protein synthesis for its execution but occurring normally in the absence of DNA synthesis or phospholipid synthesis. During stalked-cell differentiation, the flagellum and PRA reappear and the stalk elongates considerably. We show here that these events are also cell cycle dependent, requiring not only de novo protein synthesis but also DNA and phospholipid syntheses. When synchronous cells dividing 160 min after collection were used, PRA reappearance occurred at 110 min. This PRA reappearance was dependent on a phospholipid synthesis-requiring event occurring at 70 min, a DNA synthesis-requiring event occurring at 95 min, and a protein synthesis-requiring event occurring at 108 min. In the absence of net phospholipid synthesis, stalk elongation appeared more or less normal, but the stalks eventually became fragile, and by 240 min, most of the stalks had broken off, leaving only stubs attached to the cell body.

Role of the flagellum in cell-cycle-dependent expression of bacteriophage receptor activity in Caulobacter crescentus

The rate of adsorption of Caulobacter bacteriophage phi CbK to Caulobacter crescentus is dependent on the structural integrity of the flagellum. Cells lacking part or all of the flagellum because of either mutation or mechanical shear were defective in adsorption, and the extent of the defect in adsorption reflected the amount of flagellar structure missing. Maximal adsorption rates were also dependent on cellular motility and energy metabolism, since adsorption to cells with paralyzed flagella was slower than adsorption to motile cells and inhibition of cellular energy metabolism with azide also reduced adsorption rates, even for nonmotile cells. Nevertheless, the flagellum is not the receptor for phage phi CbK, since flagellumless mutants adsorbed phi CbK at detectable rates. While some portion of the fluctuation in the phi CbK receptor activity during the C. crescentus cell cycle can be ascribed to the periodicity of flagellar loss and reappearance, the phage receptor activity remaining in flagellumless mutants was periodic in the cell cycle. Therefore, the periodic expression of phage receptor activity is an intrinsic property of the C. crescentus cell cycle, although the amplitude of the oscillation may be altered by the periodic expression of flagellar motility.

An rpoN-like gene of Alcaligenes eutrophus and Pseudomonas facilis controls expression of diverse metabolic pathways, including hydrogen oxidation

Pleiotropic mutants of Alcaligenes eutrophus with the phenotype Hno- have been characterized previously. They are deficient in several diverse metabolic activities, including hydrogen oxidation, nitrate and urea assimilation, denitrification, and various substrate transport systems. Phenotypically similar mutants were identified among hydrogenase-deficient strains of Pseudomonas facilis. The Tn5-labeled hno gene was cloned from a genomic DNA library of A. eutrophus and used to identify the corresponding unimpaired wild-type DNA sequence. The recombinant plasmid pCH148 contained an insert of 12.3 kilobase pairs and was shown to restore the Hno+ phenotype to mutants of A. eutrophus and P. facilis. A cosmid isolated from a DNA library of P. facilis also exhibited intergeneric Hno-complementing activity. The cloned hno loci from both organisms showed DNA homology by Southern blot hybridization. A subclone of pCH148 which contained a 6.5-kilobase-pair insert was constructed. The resulting hybrid, pCH170, not only was able to complement Hno- mutants but also relieved glutamine auxotrophy in NtrA- mutants of enteric bacteria. This suggests that the hno gene product from A. eutrophus is functionally similar to the NtrA protein, which has been identified as a novel sigma factor (sigma 54) of RNA polymerase.

Regulation of the galactose-inducible lac operon and the histidine utilization operons in pts mutants of Klebsiella aerogenes

Galactose appears to be the physiological inducer of the chromosomal lac operon in Klebsiella aerogenes. Both lactose and galactose are poor inducers in strains having a functional galactose catabolism (gal) operon, but both are excellent inducers in gal mutants. Thus the slow growth of K. aerogenes on lactose reflects the rapid degradation of the inducer. Several pts mutations were characterized and shown to affect both inducer exclusion and permanent catabolite repression. The beta-galactosidase of pts mutants cannot be induced at all by lactose, and pts mutants appear to have a permanent and constitutive inducer exclusion phenotype. In addition, pts mutants show a reduced rate of glucose metabolism, leading to slower growth on glucose and a reduced degree of glucose-mediated permanent catabolite repression. The crr-type pseudorevertants of pts mutations relieve the constitutive inducer exclusion for lac but do not restore the full level of glucose-mediated permanent catabolite repression and only slightly weaken the glucose-mediated inducer exclusion. Except for weakening the glucose-mediated permanent catabolite repression, pts and crr mutations have no effect on expression of the histidine utilization (hut) operons.

RNA polymerase as a repressor of transcription in the hut(P) region of mutant Klebsiella aerogenes histidine utilization operons

Mutants of Klebsiella aerogenes able to express the hutUH operon in the absence of positive effectors were isolated and characterized. These mutations improve the hutUH promoter (PUH) by changing the -10 region to match the consensus sequence more closely. These mutations also affect another, oppositely oriented promoter in this region, PC. Although the mutations lie far outside PC, they cause PC to be inactive, apparently because binding of RNA polymerase to the PUH promoter blocks the overlapping PC site. Thus, in the mutants, RNA polymerase bound at the strong (mutant) PUH site effectively repress the PC promoter.

Klebsiella pneumoniae origin of replication (oriC) is not active in Caulobacter crescentus, Pseudomonas putida, and Rhodobacter sphaeroides

A DNA fragment carrying genes encoding the conjugal transfer system of the broad host range plasmid RK2 was inserted into a plasmid carrying the chromosomal origin of replication (oriC) from Klebsiella pneumoniae. The resulting plasmid, pEON1, was readily transferred between gram-negative bacteria and carried two potential origins of replication: oriC and the replication origin from pBR322 (oriPBR). Although pEON1 could be transferred to Caulobacter crescentus, Pseudomonas putida, and Rhodobacter sphaeroides, pEON1 was not maintained in these strains. However, an oriC-containing plasmid was maintained in these nonenteric bacteria when an RK2 origin of replication was present on the plasmid. Thus, the inability of pEON1 to be established in a nonenteric bacterium represents a failure of oriC to function as an origin of replication rather than a toxic effect of oriC. The initiation potential of the chromosomal origin of replication from K. pneumoniae appears to be realized only in enteric bacteria.

Bidirectional promoter in the hut(P) region of the histidine utilization (hut) operons from Klebsiella aerogenes

The hut(P) region (i.e., the region responsible for regulation of hutUH expression) of the Klebsiella aerogenes histidine utilization (hut) operons contains a bidirectional promoter. One transcript from this promoter encodes the hutUH operon; the role of the oppositely directed transcript is unknown, although it appears to be involved in regulating hutUH expression (A.J. Nieuwkoop, S.A. Boylan, and R.A. Bender, J. Bacteriol. 159:934-939, 1984). A 247-base-pair (bp) fragment containing hut(P) carries two RNA-polymerase-binding sites agree with the start sites of the two transcripts produced from hut(P) DNA in vitro and in vivo. The binding sites share a 4-bp region, suggesting that occupancy of the regulatory site precludes occupancy of the hutUH promoter, and vice versa. In the absence of positive effectors, the binding to the site responsible for hutUH transcription is weaker than the binding to the site responsible for regulation. The nucleotide sequence of the 250-bp fragment containing hut(P) contains two possible matches to the consensus sequence for Escherichia coli promoters, a better and worse match, corresponding in position to the stronger and weaker RNA-polymerase-binding sites, respectively. The sequence also contains a region similar to the consensus sequence for binding of the catabolite gene activator protein of E. coli. A sequence similar to the consensus for Ntr-dependent promoters was also found, overlapping both RNA-polymerase-binding sites, but it is not a functional promoter. Finally, an initiation codon preceded by a Shine-Dalgarno consensus sequence and followed by an open reading frame identifies a probable start of the hutU gene coding sequences.

Periodic synthesis of phospholipids during the Caulobacter crescentus cell cycle

Net phospholipid synthesis is discontinuous during the Caulobacter crescentus cell cycle with synthesis restricted to two discrete periods. The first period of net phospholipid synthesis begins in the swarmer cell shortly after cell division and ends at about the time when DNA replication initiates. The second period of phospholipid synthesis begins at a time when DNA replication is about two-thirds complete and ends at about the same time that DNA replication terminates. Thus, considerable DNA replication, growth, and differentiation (stalk growth) occur in the absence of net phospholipid synthesis. In fact, when net phospholipid synthesis was inhibited by the antibiotic cerulenin through the entire cell cycle, both the initiation and the elongation phases of DNA synthesis occurred normally. An analysis of the kinetics of incorporation of radioactive phosphate into macromolecules showed that the periodicity of phospholipid synthesis could not have been detected by pulse-labeling techniques, and only an analysis of cells prelabeled to equilibrium allowed detection of the periodicity. Equilibrium-labeled cells also allowed determination of the absolute amount of phosphorus-containing macromolecules in newborn swarmer cells. These cells contain about as much DNA as one Escherichia coli chromosome and about four times as much RNA as DNA. The amount of phosphorus in phospholipids is about one-seventh of that in DNA, or about 3% of the total macromolecular phosphorus.

Recombination deficient mutant of Caulobacter crescentus

A recombination-deficient (Rec-) strain of Caulobacter crescentus has been isolated from a collection of mutants sensitive to ultraviolet irradiation. The Rec- mutant fails to give recombinants following phi Cr30-mediated generalized transduction or following RP4-mediated conjugation. The recombination frequency in the Rec- strain is at least 5000-fold lower than in the wild type strains. The Rec- mutant is indistinguishable from wild type in terms of morphology, growth rate, viability, and phage sensitivities, differing only in properties known to be associated with recA-type mutations in other organisms: recombination frequency, ultraviolet sensitivity, and Weigle reactivation. The map location of the rec-526 allele has not been identified, but rec-526 can be cotransferred with the fla-169 mutation by RP4-mediated conjugation at low frequency. This apparent linkage has been used to move the rec mutation to other strains. The Rec- mutant resembles recA strains of other organisms and provides a healthy strain severely deficient in recombination for use in complementation and cloning studies involving C. crescentus.

Ultraviolet mutagenesis and inducible DNA repair in Caulobacter crescentus

The ability to reactivate ultraviolet (UV) damaged phage phi CbK (W-reactivation) is induced by UV irradiation of Caulobacter crescentus cells. Induction of W-reactivation potential is specific for phage phi CbK, requires protein synthesis, and is greatly reduced in the presence of the rec-526 mutation. The induction signal generated by UV irradiation is transient, lasting about 1 1/2-2 h at 30 degrees C; if chloramphenicol is present during early times after UV irradiation, induction of W-reactivation does not occur. Induction is maximal when cells are exposed to 5-10 J/m2 of UV, a dose that also results in considerable mutagenesis of the cells. Taken together, these observations demonstrate the existence of a UV inducible, protein synthesis requiring, transiently signalled, rec-requiring DNA repair system analogous to W-reactivation in Escherichia coli. In addition, C. crescentus also has an efficient photoreactivation system that reverses UV damage in the presence of strong visible light.

Regulation of hutUH operon expression by the catabolite gene activator protein-cyclic AMP complex in Klebsiella aerogenes

RNA polymerase transcribed the hutUH operon of Klebsiella aerogenes if the catabolite gene activator protein (CAP) and cyclic AMP (cAMP) were present or if the DNA template was derived from a promoter mutant in which hutUH expression was independent of the need for positive effectors. In the absence of CAP or cAMP, not only was hutUH transcription absent, but transcription in the opposite direction (toward hutC) was initiated at a site (pC) ca. 70 base pairs from the site (pUH) of hutUH mRNA initiation. When the pC promoter was cloned in front of a promoterless galK gene, active expression of galK was observed. Thus, the pC promoter is active in vivo as well as in vitro. Transcription from pUH and pC may be mutually exclusive, with the major effect of CAP and cAMP being to prevent transcription from pC, thus relieving the antagonistic effect on transcription from pUH. This "double-negative" control by CAP-cAMP is supported by two observations: (i) CAP-cAMP was unable to activate transcription from pUH if RNA polymerase had been previously bound to pC and (ii) a mutation that allowed transcription from pUH in the absence of positive effectors simultaneously eliminated the activity of pC. An alternative model, in which CAP-cAMP is required for pUH expression and RNA polymerase binding at pC serves to modulate this control in some unknown way, is also considered. The physiological role of the transcript from pC other than regulation of pUH is unknown.

Transposon Tn5 encodes streptomycin resistance in nonenteric bacteria

Strains of Caulobacter crescentus, Pseudomonas putida, Acinetobacter calcoaceticus, Rhizobium meliloti, and Rhodopseudomonas sphaeroides carrying the kanamycin resistance-encoding transposon Tn5 were 15 to 500 times more resistant to streptomycin than transposon-free strains. The streptomycin resistance determinant, which is separable from the kanamycin resistance determinant of Tn5, was not expressed in Escherichia coli or Klebsiella aerogenes.

Use of bacteriophage P1 as a vector for Tn5 insertion mutagenesis

Infection of a strain lysogenic for bacteriophage P1 CM with P1::Tn5 followed by simultaneous selection for the chloroamphenicol resistance associated with the resident prophage and the kanamycin resistance associated with Tn5 results in a large number of independent Tn5 insertion mutations. This superinfection-selection protocol is a fast, easy, and safe way to isolate null mutations in enteric bacteria without generating unwanted cryptic mutations elsewhere in the genome.

Genetic and physical maps of Klebsiella aerogenes genes for histidine utilization (hut)

Deletion derivatives of the hut-containing plasmid pCB101 were tested against point mutants defective in individual genes of the histidine utilization (hut) operons using a complementation/recombination assay. Location of the genes of the right operon, hutU and hutH, was confirmed by direct assay of the gene products, urocanase and histidase; location of the repressor gene was identified by measuring the ability of the plasmid-carried genes to repress the formation of histidase from a chromosomal location. The analysis of eight deletion plasmids unambiguously confirms the map order of the hut genes as hutI-G-C-U-H, and demonstrates that, in Klebsiella aerogenes, the hutU and hutH genes are transcribed from their own promoter. In addition, the genetic map of hut can be aligned with the restriction map of the hut DNA in plasmid pCB101. One of the deletion plasmids studied apparently encodes a defective histidase subunit that is trans-dominant to active histidase. Another deletion, which completely removes the left operon, hutIG, allows high level expression of the hutUH operon and thus overproduction of a toxic intermediate.

A restriction enzyme cleavage map of the histidine utilization (hut) genes of Klebsiella aerogenes and deletions lacking regions of hut DNA

The histidine utilization (hut) operons of Klebsiella aerogenes were cloned into pBR322. The hut genes are wholly contained on a 7.9 kilobase pair fragment bounded by HindIII restriction sites and expression of hut is independent of the orientation of the fragment with respect to pBR322. A restriction map locating the 27 cleavage sites within hut for the enzymes, HindIII, PvuII, SalI, BglII, KpnI, PstI, SmaI, AvaI, and BamHI was deduced. Several of the cleavage sites for the enzymes HaeIII and HinfI were also mapped. A set of deletion plasmids was isolated by removing various restriction fragments from the original plasmid. These deletions were characterized and were used to assist in mapping restriction sites. This physical characterization of hut DNA opens the way for genetic and molecular analysis of the regulation of hut gene expression in vitro as well as in vivo.

Nitrogen regulation system of Klebsiella aerogenes: the nac gene

In Klebsiella aerogenes, the product of a his-linked gene, nac, appears to play a crucial role in tying the synthesis of enzymes activated or repressed by ammonia deprivation, such as histidase and glutamate dehydrogenase, to the known regulators of nitrogen assimilation, the products of glnG and glnF.