Mutation of gene encoding regulatory polypeptide of aspartate carbamoyltransferase

Studies on flavans. 1. Facile synthesis of (+/-)-7-hydroxy-3',4'-methylenedioxyflavan and (+/-)-4'-hydroxy-7-methoxyflavan by a BF3.Et2O-mediated pyran cyclization

A facile approach for the synthesis of flavans was developed by employing a BF3.Et2O-catalyzed pyran cyclization in an aprotic polar solvent as a key step, by which concise total syntheses of (+/-)-7-hydroxy-3',4'-methylenedioxyflavan (1) and (+/-)-4'-hydroxy-7-methoxyflavan (2), two naturally occurring flavans, were achieved.

Analysis of protein synthesis rates after initiation of chromosome replication in Escherichia coli

The aim of this study was to investigate whether the synthesis rates of some proteins change after the initiation of replication in Escherichia coli. An intR1 strain, in which chromosome replication is under the control of an R1 replicon integrated into an inactivated oriC, was used to synchronize chromosome replication, and the rates of protein synthesis were analyzed by two-dimensional polyacrylamide gel electrophoresis of pulse-labeled proteins. Computerized image analysis was used to search for proteins whose expression levels changed at least threefold after initiation of a single round of chromosome replication, which revealed 7 out of about 1,000 detected proteins. The various synthesis rates of three of these proteins turned out to be caused by unbalanced growth and the synthesis of one protein was suppressed in the intR1 strain. The rates of synthesis of the remaining three could be correlated only to the synchronous initiation of replication. These three proteins were analyzed by peptide mass mapping and appeared to be the products of the dps, gapA, and pyrI genes. Thus, the expression of the vast majority of proteins is not influenced by the state of chromosome replication, and a possible role of the replication-associated expression changes of the three identified proteins in the cell cycle is not clear.

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.

Crystal structure of CTP-ligated T state aspartate transcarbamoylase at 2.5 A resolution: implications for ATCase mutants and the mechanism of negative cooperativity

The X-ray crystal structure of CTP-ligated T state aspartate transcarbamoylase has been refined to an R factor of 0.182 at 2.5 A resolution using the computer program X-PLOR. The structure contains 81 sites for solvent and has rms deviations from ideality in bond lengths and bond angles of 0.018 A and 3.722 degrees, respectively. The cytosine base of CTP interacts with the main chain carbonyl oxygens of rTyr-89 and rIle-12, the main chain NH of rIle-12, and the amino group of rLys-60. The ribose hydroxyls form polar contacts with the amino group of rLys-60, a carboxylate oxygen of rAsp-19, and the main chain carbonyl oxygen of rVal-9. The phosphate oxygens of CTP interact with the amino group of rLys-94, the hydroxyl of rThr-82, and an imidazole nitrogen of rHis-20. Recent mutagenesis experiments evaluated in parallel with the structure reported here indicate that alterations in the hydrogen bonding environment of the side chain of rAsn-111 may be responsible for the homotropic behavior of the pAR5 mutant of ATCase. The location of the first seven residues of the regulatory chain has been identified for the first time in a refined ATCase crystal structure, and the proximity of this portion of the regulatory chain to the allosteric site suggests a potential role for these residues in nucleotide binding to the enzyme. Finally, a series of amino acid side chain rearrangements leading from the R1 CTP allosteric to the R6 CTP allosteric site has been identified which may constitute the molecular mechanism of distinct CTP binding sites on ATCase.

Structure-function relationship in allosteric aspartate carbamoyltransferase from Escherichia coli. I. Primary structure of a pyrI gene encoding a modified regulatory subunit

In a previous article, we have identified a lambda bacteriophage directing the synthesis of a modified aspartate carbamoyltransferase lacking substrate-co-operative interactions and insensitive to the feedback inhibitor CTP. These abnormal properties were ascribed to a mutation in the gene pyrI encoding the regulatory polypeptide chain of the enzyme. We now report the sequence of the mutated pyrI and show that, during the generation of this pyrBI-bearing phage, six codons from lambda DNA have been substituted for the eight terminal codons of the wild-type gene. A model is presented for the formation of this modified pyrI gene during the integrative recombination of the parental lambda phage with the Escherichia coli chromosome. An accompanying paper emphasizes the importance of the carboxy-terminal end of the regulatory chain for the homotropic and heterotropic interactions of aspartate carbamoyltransferase.

Structure-function relationship in allosteric aspartate carbamoyltransferase from Escherichia coli. II. Involvement of the C-terminal region of the regulatory chain in homotropic and heterotropic interactions

The modified aspartate transcarbamylase (ATCase) encoded by the transducing phage described by Cunin et al. has been purified to homogeneity. In this altered form of enzyme (pAR5-ATCase) the last eight amino acids of the C-terminal end of the regulatory chains are replaced by a sequence of six amino acids coded for by the lambda DNA. This modification has very informative consequences on the allosteric properties of ATCase. pAR5-ATCase lacks the homotropic co-operative interactions between the catalytic sites for aspartate binding and is "frozen" in the R state. In addition, this altered form of enzyme is insensitive to the physiological feedback inhibitor CTP, in spite of the fact that this nucleotide binds normally to the regulatory sites. Conversely, pAR5-ATCase is fully sensitive to the activator ATP. However, this activation is limited to the extent of the previously described "primary effect" as expected from an ATCase form "frozen" in the R state. These results emphasize the importance of the three-dimensional structure of the C-terminal region of the regulatory chains for both homotropic and heterotropic interactions. In addition, they indicate that the primary effects of CTP and ATP involve different features of the regulatory chain-catalytic chain interaction area.

Evolutionary divergence of genes for ornithine and aspartate carbamoyl-transferases--complete sequence and mode of regulation of the Escherichia coli argF gene; comparison of argF with argI and pyrB

The complete nucleotide sequence of argF is presented, together with that of an operator-constitutive mutant. ArgF is compared with the other gene coding for ornithine carbamoyltransferase (OTCase) in E. coli K-12, argI, and with pyrB, encoding the catalytic monomer of aspartate carbamoyltransferase (ATCase). ArgF and argI appear very closely related having emerged from a relatively recent ancestor gene. The relationship between OTCase and ATCase appears more distant. Nevertheless, the homology observed between the two proteins (mainly in the polar domain) suggests a common origin.

Nucleotide sequence of the structural gene (pyrB) that encodes the catalytic polypeptide of aspartate transcarbamoylase of Escherichia coli

The deoxyribonucleotide sequence of pyrB, the cistron encoding the catalytic subunit of aspartate transcarbamoylase (carbamoylphosphate: L-aspartate carbamoyltransferase, EC 2.1.3.2), has been determined. The pyrB gene encodes a polypeptide of 311 amino acid residues initiated by an NH2-terminal methionine that is not present in the catalytically active polypeptide. The DNA sequence analysis revealed the presence of an eight-amino-acid sequence beginning at Met-219 that was not detected in previous analyses of amino acid sequence. This octapeptide sequence provides an additional component of the disordered loop in the equatorial domain of the catalytic polypeptide. It had been found previously that the catalytic polypeptide is expressed from a bicistronic operon that also produces the regulatory polypeptide encoded by pyrI. A single transcriptional control region precedes the structural gene of the catalytic polypeptide and a simple 15-base-pair region separates its COOH terminus from the structural gene of the regulatory polypeptide. The chain-terminating codon of the catalytic polypeptide may contribute to the ribosomal binding site for the regulatory polypeptide and thus assist coordinate expression of the two cistrons.

The organization and regulation of the pyrBI operon in E. coli includes a rho-independent attenuator sequence

1. The two polypeptide chains that comprise aspartate carbamoyltransferase in Escherichia coli are encoded by adjacent cistrons expressed in the order, promoter-leader-catalytic cistron-regulatory cistron (p-leader-pyrBI). These two cistrons and their single control region have been cloned as a 2,800 base pair (bp) fragment (The minimal coding requirement for the catalytic and regulatory polypeptides is about 1,350 bp plus control regions). The genes contained by this fragment are subject to normal repression controls and thus possess the intact control regions. 2. By deleting an internal fragment with specific restriction endonucleases, it was possible to construct shortened fragments which no longer produced the regulatory polypeptide. In these cases the expression of the catalytic cistron was normal and subject to repression upon growth in the presence of uracil. Since the pyrB cistron retained transcriptional control, the regulatory polypeptide was not required for expression or control of the catalytic cistron. As expected, the catalytic trimer (Mr = 100,000 daltons) from these deletion mutants had no effector response nor did it exhibit homotropic kinetics for aspartate. The enzyme was identical to the c3 trimer purified from the native holoenzyme by neohydrin dissociation. 3. Insertion of Mu d1(lac Apr) into the structural region of pyrB had a negative effect on the expression of pyrI. This supports the idea that the catalytic and regulatory polypeptide chains of aspartate carbamoyl-transferase are encoded by a single bicistronic operon. Detailed restriction analysis of the cloned pyrBI region has produced a genetic map of restriction sites which is colinear with the published amino acid sequences of the two polypeptides. These maps indicate that the 3'-terminus of the catalytic cistron is adjacent to the 5'-terminus of the regulatory cistron and separated by 10-20 bp. 4. DNA sequence analysis of the 5'-proximal regions of pyrBI revealed that an extensive leader sequence separated the promoter and first structural gene pyrB. This leader of approximately 150 bp contains an attenuator sequence and the translational signals required for the production of a leader polypeptide of 43 amino acids. In this paper we describe the structural organization of pyrBI, and provide a detailed analysis of its regulatory region including its DNA sequence.

Genes encoding Escherichia coli aspartate transcarbamoylase: the pyrB-pyrI operon

In both Escherichia coli and Salmonella typhimurium there is approximately balanced synthesis of the six catalytic and six regulatory polypeptide chains of the regulatory enzyme aspartate transcarbamoylase (carbamoylphosphate:L-aspartate carbamoyltransferase, EC 2.1.3.2). This control is achieved by the contiguous pyrB and pyrI genes, which encode the catalytic and regulatory chains, respectively. Evidence for this single transcriptional unit was obtained by a study of various deletion mutations and from the DNA sequence of the intercistronic region between pyrB and pyrI. One pyrB deletion, pyrB748, produced a normal level of regulatory chains even though it removed a substantial portion of the pyrB gene. Another deletion, pyrB740, shares a similar terminus at one end within pyrB, but the promoter region is removed. In this deletion mutation, there is no production of the regulatory polypeptide, indicating that a single region adjacent to pyrB controls transcription of pyrI as well. Molecular cloning and subsequent DNA analysis demonstrated that the pyrB and pyrI genes are contiguous with pyrI as the distal gene in the operon. The cistrons are separated by a 15-nucleotide untranslated region containing a sequence capable of interacting with the 16S ribosomal RNA and allowing translation of the pyrI cistron.