Glutamine synthetase cascade: enrichment of uridylyltransferase in Escherichia coli carrying hybrid ColE1 plasmids

Genome-wide screening of genes affecting glycogen metabolism in Escherichia coli K-12

A systematic and comprehensive gene-disrupted mutant collection of E. coli K-12 was used to identify genes whose deletions affect glycogen accumulation. Of the 3985 non-essential gene mutants of the collection, 35 displayed a glycogen-excess phenotype, whereas 30 displayed either glycogen-less or glycogen-deficient phenotypes. The genes whose deletions affect glycogen accumulation were classified into various functional categories, including energy production, envelope composition and integrity, protein translation and stability, transport of inorganic ions and nucleotides, and metabolism of carbohydrates and amino acids. The overall data indicate that glycogen metabolism is highly interconnected with a wide variety of cellular processes in E. coli.

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

The role of uridylyltransferase in the control of Klebsiella pneumoniae nif gene regulation

The glnD gene in enteric bacteria encodes a uridylyltransferase/uridylyl-removing enzyme which acts as the primary nitrogen sensor in the nitrogen regulation (Ntr) system. We have investigated the role of this enzyme in transcriptional regulation of nitrogen fixation genes in Klebsiella pneumoniae by cloning glnD from this organism and constructing a null mutant by insertional inactivation of the chromosomal gene using the omega interposon. K. pneumoniae glnD encodes a 102.3 kDa polypeptide which is highly homologous to the predicted products of both Escherichia coli glnD and Azotobacter vinelandii nfrX. The glnD-omega mutant was unable to uridylylate PII and was altered in adenylylation/deadenylylation of glutamine synthetase. Uridylyltransferase was required for derepression of ntr-regulated promoters such as glnAp2 and pnifL but was not involved in the nif-specific response to changes in nitrogen status mediated by the nifL product. We conclude that a separate, as yet uncharacterised, nitrogen control system may be responsible for nitrogen sensing by NifL.

The product of the nitrogen fixation regulatory gene nfrX of Azotobacter vinelandii is functionally and structurally homologous to the uridylyltransferase encoded by glnD in enteric bacteria

We sequenced the nitrogen fixation regulatory gene nfrX from Azotobacter vinelandii, mutations in which cause a Nif- phenotype, and found that it encodes a 105-kDa protein (NfrX), the N terminus of which is highly homologous to that of the uridylyltransferase-uridylyl-removing enzyme encoded by glnD in Escherichia coli. In vivo complementation experiments demonstrate that the glnD and nfrX products are functionally interchangeable. A vinelandii nfrX thus appears to encode a uridylyltransferase-uridylyl-removing enzyme, and in this paper we report the first sequence of such a protein. The Nif- phenotype of nfrX mutants can be suppressed by a second mutation in a recently identified nifL-like gene immediately upstream of nifA in A. vinelandii. NifL mediates nif regulation in response to the N status in A. vinelandii, presumably by inhibiting NifA activator function as occurs in Klebsiella pneumoniae; thus, one role of NfrX is to modify, either directly or indirectly, the activity of the nifL product.

Effect of some D-amino acids on the steady-state level of glutamine synthetase in Escherichia coli

D-Glutamate can elicit an increase in the specific activity of glutamine synthetase (GS) when added to cells growing in the presence of high ammonia nitrogen. This effect is independent of glutamate dehydrogenase or glutamate synthase activities and could not be provoked by the addition of the various metabolites which participate in the regulation of GS in the covalent modification system. Neither could an increase in GS level be elicited by addition of any of the D-amino acids which function as allosteric effectors or inhibitors of GS activity. The increase in GS level could also be provoked by addition of D-lysine, D-threonine, or glycine to cells growing in an ammonia-rich medium. The increase in GS level generated by a mixture of D-glutamate, D-lysine, D-threonine, and glycine approximates the increase in GS level observed during step-down of a wild-type Escherichia coli culture from ammonia-sufficient to ammonia-limited growth conditions. Studies with mutants exhibiting alterations in GS regulation indicated that the increase elicited by the addition of D-amino acids depends on the presence of the wild-type glnD allele, although no direct correlation between a positive response and the state of adenylylation of GS can be made.

Catabolism and nitrogen control in Escherichia coli

It would appear from these studies that nitrogen control reflects the catabolic capacity of the cell and that utilizable nitrogen sources and some carbon sources are, to some extent, in competition for this capacity. The series of catabolic events initiated by addition of D-amino acids or by growth on aldol sugars, in the presence of ammonia nitrogen in the growth medium, provide an opportunity for study of the positive aspect of nitrogen control under conditions where negative control predominates. This approach may eventually clarify the apparent interactions between the modification cascade components, PII and UT/UR, with the nitrogen regulatory gene, glnG. The utilization of nutrients by E. coli seems less a matter of energy than of expeditious use of whatever is offered in the diet. A comparison of the rate of increase of GS on cultural downshift with the rate of increase following D-glutamate addition would suggest that control by nitrogen limitation is about eight times more effective than positive activation by D-glutamate in the presence of ammonia nitrogen. This observation is consistent with the finding of an additive effect for the D-amino acids which can function as positive activators in GS regulation. It has been demonstrated for the wild-type organism that the increase in GS level generated by a mixture of D-glutamate, D-lysine, D-threonine, and glycine approximates the increase in GS level observed during step-down of the culture from an ammonia-sufficient to an ammonia-limited condition. This observation further supports the physiologic relevance of the effect of D-amino acids in nitrogen control and suggests that the apparent derepression of GS observed upon exhaustion of the ammonia nitrogen supply represents a composite of positive activation generated as alternative catabolic functions assume a greater importance. As might be expected, addition of D-glutamate to cells at the point of ammonia exhaustion had no additional positive effect. Following a downshift from glucose-ammonia-glutamine to glucose-glutamine cultural conditions, only the level of GS increases during the initial 60-minute observation period. This finding suggests that glutamine catabolism may, like D-threonine, D-lysine, and glycine, bypass the positive activation of GDH and GAT controls. The likely possibility in that the increases observed for GAT and GDH depend on D-glutamate as specific inducer. There are several instances where D-amino acids function as inducers of L-amino acid dehydrogenases and where amino acid racemase activity is directly coupled to flavoprotein dehydrogenases.(ABSTRACT TRUNCATED AT 400 WORDS)

The role of adenylyltransferase and uridylyltransferase in the regulation of glutamine synthetase in Escherichia coli

The regulation of GS activity involves two nucleotidylation cycles, the uridylylation cycle of PII and the adenylylation cycle of GS, which are catalyzed by two converter enzymes, uridylyltransferase and adenylyltransferase, respectively. The converter enzymes sense the fluctuation in the availability of nitrogen and accordingly regulate the activity of GS. On the other hand, the posttranslational modification of GS is tightly coupled to the transcriptional regulation of the glnA gene by unmodified PII protein acting as a repressor in the GS synthesis. Therefore, metabolic signals perceived by uridylyltransferase are transmitted through PII to two different levels of the regulation, namely, the posttranslational level and transcriptional level. In order to study the converter enzymes which exist in extremely low concentration, the glnD and glnE genes were cloned into a plasmid vector carrying the strong, regulatable lambda phage promoter. In this way, uridylyltransferase and adenylyltransferase were overproduced to the levels approaching 800- and 500-fold, respectively. The recombinant DNA technology also enabled us to examine the transcriptional regulation of the glnD and glnE genes. The expression of these genes was slightly repressed under nitrogen-excess conditions and the repressions were more pronounced under excess nitrogen plus carbon-limiting conditions. It was found that variations of the concentration of uridylyltransferase and adenylyltransferase also affect the rate of GS synthesis. Studies with strains harboring a multicopy plasmid, pglnD or pglnE, indicate that the elevated synthesis of the converter enzymes causes the enhancement of GS synthesis. In addition, the absence of one of the converter enzymes reduces the expression of the glnA gene. The parallel relationship between the converter enzymes and GS seems to derive from the binding capacity of the converter enzymes for the unbound PII, which is a repressor for the glnA gene. Therefore, it is believed that the metabolic regulation of the glnD and glnE genes is ultimately linked to the expression of the glnA operon.

Gene-protein index of Escherichia coli K-12

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A cloned cyanobacterial gene for glutamine synthetase functions in Escherichia coli, but the enzyme is not adenylylated

The coding sequence for Anabaena 7120 glutamine synthetase [L-glutamate:ammonia ligase (ADP-forming), EC 6.3.1.1] are shown to be contained within a 7.5-kilobase-pair (kbp) HindIII fragment that has been cloned by plaque hybridization. The hybridization probe for the cyanobacterial gene was a recombinant plasmid containing the glnA gene from Escherichia coli K-12. Evidence that the cloned Anabaena fragment contains the glnA gene includes complementation of a glnA deletion mutant of E. coli and immunological identity of the enzyme produced by the cloned Anabaena fragment in E. coli with glutamine synthetase purified from Anabaena 7120. Heteroduplex analysis reveals 0.65 kbp of homology between the 7.5-kbp Anabaena 7120 fragment and an 11-kbp E. coli fragment that codes for E. coli glutamine synthetase. Studies of Anabaena glnA gene activity in E. coli suggest that the cyanobacterial gene is not repressible and that the Anabaena 7120 glutamine synthetase is not adenylylated in E. coli.