Purification, characterization, DNA sequence and cloning of a pimeloyl-CoA synthetase from Pseudomonas mendocina 35. (1/125)

A pimeloyl-CoA synthetase from Pseudomonas mendocina 35 was purified and characterized, the DNA sequence determined, and the gene cloned into Escherichia coli to yield an active enzyme. The purified enzyme had a pH optimum of approximately 8.0, Km values of 0.49 mM for pimelic acid, 0.18 mM for CoA and 0.72 mM for ATP, a subunit Mr of approximately 80000 as determined by SDS/PAGE, and was found to be a tetramer by gel-filtration chromatography. The specific activity of the purified enzyme was 77.3 units/mg of protein. The enzyme was not absolutely specific for pimelic acid. The relative activity for adipic acid (C6) was 72% and for azaleic acid (C9) was 18% of that for pimelic acid (C7). The N-terminal amino acid was blocked to amino acid sequencing, but controlled proteolysis resulted in three peptide fragments for which amino acid sequences were obtained. An oligonucleotide gene probe corresponding to one of the amino acid sequences was synthesized and used to isolate the gene (pauA, pimelic acid-utilizing A) coding for pimeloyl-CoA synthetase. The pauA gene, which codes for a protein with a theoretical Mr of 74643, was then sequenced. The deduced amino acid sequence of the enzyme showed similarity to hypothetical proteins from Archaeoglobus fulgidus, Methanococcus jannaschii, Pyrococcus horikoshii, E. coli and Streptomyces coelicolor, and some limited similarity to microbial succinyl-CoA synthetases. The similarity with the protein from A. fulgidus was especially strong, thus indicating a function for this unidentified protein. The pauA gene was cloned into E. coli, where it was expressed and resulted in an active enzyme.  (+info)

Peptidoglycan turnover during growth of a Bacillus megaterium Dap- Lys- mutant. (2/125)

The aim of this study was to ascertain whether or not the absence of cell wall growth zones, deduced from the analysis of autoradiographs of DL-[3H]mesodiaminopimelic acid pulse-labeled cells of a Dap- Lys- mutant of Bacillus megaterium, was due to a high peptidoglycan turnover. Turnover was determined in very precise experimental conditions because two kinds of turnover occurred: a low, acid-soluble turnover and a high, acid-insoluble one. The latter was detected during a chase in the culture medium when bacteria were centrifuged before treatment with trichloroacetic acid. Otherwise the acid-insoluble released material precipitated with the bacteria. In the electron microscope this material presented a globular structure and contained both peptidoglycan and teichoic acid. The acid-insoluble turnover was mainly produced by a lytic acitivity that was released into the culture medium. This thermolabile activity was not due to cell lysis. It was implicated in septum cleavage and in the detachment of wall fragments from the cell surface, but did not seem indispensable for cell elongation. The acid-soluble turnover was much weaker and seemed to be indispensable for cell elongation.  (+info)

Sphere-rod morphogenesis of Escherichia coli. (3/125)

The morphogenetic capacity of E. coli was studied by converting the rod-shaped cells into spheres and then determining whether these spheres could revert to rods. The morphogenesis of cells was followed by immobilizing them in a viscous Methocel-containing medium. Two different types of spheres were prepared: cells which retained a mechanically intact sacculus, and osmotically sensitive sphaeroplasts lacking a sacculus. The sphaeroplasts were not able to revert to rods although they were able to synthesize a new sacculus. In contrast, spheres which had retained an intact sacculus were able to reshape themselves into rods. The were also able to form new ends at (or near) the sites of the ends on the original rods.  (+info)

nag genes of Ralstonia (formerly Pseudomonas) sp. strain U2 encoding enzymes for gentisate catabolism. (4/125)

Ralstonia sp. strain U2 metabolizes naphthalene via gentisate to central metabolites. We have cloned and sequenced a 21.6-kb region spanning the nag genes. Upstream of the pathway genes are nagY, homologous to chemotaxis proteins, and nagR, a regulatory gene of the LysR family. Divergently transcribed from nagR are the genes for conversion of naphthalene to gentisate (nagAaGHAbAcAdBFCQED) (S. L. Fuenmayor, M. Wild, A. L. Boyes, and P. A. Williams, J. Bacteriol. 180:2522-2530, 1998), which except for the insertion of nagGH, encoding the salicylate 5-hydroxylase, are homologous to and in the same order as the genes in the classical upper pathway operon described for conversion of naphthalene to salicylate found in the NAH7 plasmid of Pseudomonas putida PpG7. Downstream of nahD is a cluster of genes (nagJIKLMN) which are probably cotranscribed with nagAaGHAbAcAdBFCQED as a single large operon. By cloning into expression vectors and by biochemical assays, three of these genes (nagIKL) have been shown to encode the enzymes involved in the further catabolism of gentisate to fumarate and pyruvate. NagI is a gentisate 1,2-dioxygenase which converts gentisate to maleylpyruvate and is also able to catalyze the oxidation of some substituted gentisates. NagL is a reduced glutathione-dependent maleylpyruvate isomerase catalyzing the isomerization of maleylpyruvate to fumarylpyruvate. NagK is a fumarylpyruvate hydrolase which hydrolyzes fumarylpyruvate to fumarate and pyruvate. The three other genes (nagJMN) have also been cloned and overexpressed, but no biochemical activities have been attributed to them. NagJ is homologous to a glutathione S-transferase, and NagM and NagN are proteins homologous to each other and to other proteins of unknown function. Downstream of the operon is a partial sequence with homology to a transposase.  (+info)

The metabolism of benzoate by Moraxella species through anaerobic nitrate respiration. Evidence for a reductive pathway. (5/125)

Moraxella sp. isolated from soil grows anaerobically on benzoate by nitrate respiration; nitrate or nitrite are obligatory electron acceptors, being reduced to molecular N2 during the catabolism of the substrate. This bacterium also grows aerobically on benzoate. 2. Aerobically, benzoate is metabolized by ortho cleavage of catechol followed by the beta-oxoadipate pathway. 3. Cells of Moraxella grown anaerobically on benzoate are devoid of ortho and meta cleavage enzymes; cyclohexanecarboxylate and 2-hydroxycyclohexanecarboxylate were detected in the anaerobic culture fluid. 4. [ring-U-14C]Benzoate, incubated anaerobically with cells in nitrate-phosphate buffer, gave rise to labelled 2-hydroxycyclohexanecarboxylate and adipate. When [carboxy-14C]benzoate was used, 2-hydroxycyclohexanecarboxylate was radioactive but the adipate was not labelled. A decarboxylation reaction intervenes at some stage between these two metabolites. 5. The anaerobic metabolism of benzoate by Moraxella sp. through nitrate respiration takes place by the reductive pathway (Dutton & Evans, 1969). Hydrogenation of the aromatic ring probably occurs via cyclohexa-2,5-dienecarboxylate and cyclohex-1-enecarboxylate to give cyclohexanecarboxylate. The biochemistry of this reductive process remains unclear. 6. CoA thiol esterification of cyclohexanecarboxylate followed by beta-oxidation via the unsaturated and hydroxy esters, would afford 2-oxocyclohexanecarboxylate. Subsequent events in the Moraxella culture differ from those occurring with Rhodopseudomonas palustris; decarboxylation precedes hydrolytic cleavage of the alicyclic ring to produce adipate in the former, whereas in the latter the keto ester undergoes direct hydrolytic fission to pimelate.  (+info)

The aerobic metabolism of cyclohexanecarboxylic acid by Acinetobacter anitratum. (6/125)

1. The aerobic metabolism of cyclohexanecarboxylic acid by a bacterium isolated from garden soil (Acinetobacter anitratum) was investigated. 2. Evidence for the formation of cyclohex-1-ene-1-carboxylate, 2-hydroxycyclohexanecarboxylate and pimelate when either cell suspensions or cell-free extracts were incubated in the presence of cyclohexanecarboxylic acid is presented. 3. Crude cell-free extracts required ATP, CoA, FAD and Mg2+ as cofactors for the production of pimelate from cyclohexanecarboxylic acid, suggesting the existence of an activating reaction with formation of CoA esters, in this system.  (+info)

Acyl group specificity at the active site of tetrahydridipicolinate N-succinyltransferase. (7/125)

Tetrahydrodipicolinate N-succinyltransferase (DapD) catalyzes the succinyl-CoA-dependent acylation of L-2-amino-6-oxopimelate to 2-N-succinyl-6-oxopimelate as part of the succinylase branch of the meso-diaminopimelate/lysine biosynthetic pathway of bacteria, blue-green algae, and plants. This pathway provides meso-diaminopimelate as a building block for cell wall peptidoglycan in most bacteria, and is regarded as a target pathway for antibacterial agents. We have solved the X-ray crystal structures of DapD in ternary complexes with pimelate/succinyl-CoA and L-2-aminopimelate with the nonreactive cofactor analog, succinamide-CoA. These structures define the binding conformation of the cofactor succinyl group and its interactions with the enzyme and place its thioester carbonyl carbon in close proximity to the nucleophilic 2-amino group of the acceptor, in support of a direct attack ternary complex mechanism. The acyl group specificity differences between homologous tetrahydrodipicolinate N-acetyl- and N-succinyltransferases can be rationalized with reference to at least three amino acids that interact with or give accessible active site volume to the cofactor succinyl group. These residues account at least in part for the substrate specificity that commits metabolic intermediates to either the succinylase or acetylase branches of the meso-diaminopimelate/lysine biosynthetic pathway.  (+info)

Ribonucleic acid in a "membrane" fraction of Escherichia coli and its relation to cell-wall synthesis. (8/125)

Suit, Joan C. (The University of Texas M. D. Anderson Hospital and Tumor Institute, Houston). Ribonucleic acid in a "membrane" fraction of Escherichia coli and its relation to cell-wall synthesis. J. Bacteriol. 84:1061-1070. 1962.-A small amount of ribonucleic acid (RNA) was found in a "membrane" fraction prepared from osmotically sensitized Escherichia coli. It exhibited an elevated metabolic activity in that it attained the highest specific activity of any RNA in subcellular fractions of logarithmic-phase cells or spheroplasts prepared from logarithmic-phase cells which had been allowed to incorporate P(32) briefly. The metabolic activity of this RNA, in terms of P(32) incorporation, was found to be independent of cell-wall synthesis in the diaminopimelic acid (DAP)-less mutant, E. coli W 173-25, but was inhibited by penicillin in both this strain and in E. coli B. The latter effect is considered to be a result of other complex inhibitions of cellular metabolism by the antibiotic. The development of sensitivity to osmotic shock, capability of recovery, and synthesis of macromolecules in penicillin-treated and DAP-starved cultures, under these conditions, is described.  (+info)

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