Mechanistic studies of a protonolytic organomercurial cleaving enzyme: bacterial organomercurial lyase

Mechanistic studies of the protonolytic carbon-mercury bond cleavage by organomercurial lyase from Escherichia coli (R831) suggest that the reaction proceeds via an SE2 pathway. Studies with stereochemically defined substrates cis-2-butenyl-2-mercuric chloride (1) and endo-norbornyl-2-mercuric bromide (2) reveal that a high degree of configurational retention occurs during the bond cleavage, while studies with exo-3-acetoxynortricyclyl-5-mercuric bromide (3) and cis-exo-2-acetoxy-bicyclo[2.2.1]hept-5-enyl-3-mercuric bromide (4) show that the protonolysis proceeds without accompanying skeletal rearrangement. Kinetic data for the enzymatic reactions of cis-2-butenyl-2-mercuric chloride (1) and trans-1-propenyl-1-mercuric chloride (6) indicate that these substrates show enhanced reaction rates of ca. 10-200-fold over alkylvinylmercurials and unsubstituted vinylmercurials, suggesting that the olefinic methyl substituent may stabilize an intermediate bearing some positive charge. Enzymatic reaction of 2-butenyl-1-mercuric bromide (5) yields a 72/23/5 mixture of 1-butene/trans-2-butene/cis-2-butene, indicative of intervening SE2' cleavage. The observation of significant solvent deuterium isotope effects at pH 7.4 of Vmax (H2O)/Vmax(D2O) = 2.1 for cis-2-butenyl-2-mercuric chloride (1) turnover and Vmax(H2O)/Vmax(D2O) = 4.9 for ethylmercuric chloride turnover provides additional support for a kinetically important proton delivery. Finally, the stoichiometric formation of butene and Hg(II) from 1 and methane and Hg(II) from methylmercuric chloride eliminates the possibility of an SN1 solvolytic mechanism. As the first well-characterized enzymatic reaction of an organometallic substrate and the first example of an enzyme-mediated SE2 reaction the organomercurial lyase catalyzed carbon-mercury bond cleavage provides an arena for investigating novel enzyme structure-function relationships.     

Glycinamide ribonucleotide synthetase from Escherichia coli: cloning, overproduction, sequencing, isolation, and characterization

The purD gene of Escherichia coli encoding the enzyme glycinamide ribonucleotide (GAR) synthetase, which catalyzes the conversion of phosphoribosylamine (PRA), glycine, and MgATP to glycinamide ribonucleotide, MgADP, and Pi, has been cloned and sequenced. The protein, as deduced by the structural gene sequence, contains 430 amino acids and has a calculated Mr of 45,945. Construction of an overproducing strain behind a lambda pL promoter allowed a 4-fold purification of the protein to homogeneity. N-Terminal sequence analysis and comparison of the sequence with those of other GAR synthetases confirm the amino acid sequence deduced from the gene sequence. Initial velocity studies and product and dead-end inhibition studies are most consistent with a sequential ordered mechanism of substrate binding and product release in which PRA binds first followed by MgATP and then glycine; Pi leaves first, followed by loss of MgADP and finally GAR. Incubation of [18O]glycine, ATP, and PRA results in quantitative transfer of the 18O to Pi. GAR synthetase is very specific for its substrate glycine.     

Formylglycinamide ribonucleotide synthetase from Escherichia coli: cloning, sequencing, overproduction, isolation, and characterization

The purL gene of Escherichia coli encoding the enzyme formylglycinamidine ribonucleotide (FGAM) synthetase which catalyzes the conversion of formylglycinamide ribonucleotide (FGAR), glutamine, and MgATP to FGAM, glutamate, ADP, and Pi has been cloned and sequenced. The mature protein, as deduced by the structural gene sequence, contains 1628 amino acids and has a calculated Mr of 141,418. Comparison of the purL control region to other pur loci control regions reveals a common region of dyad symmetry which may be the binding site for the "putative" repressor protein. Construction of an overproducing strain permitted purification of the protein to homogeneity. N-Terminal sequence analysis and comparison of glutamine binding domain sequences (Ebbole & Zalkin, 1987) confirm the amino acid sequence deduced from the gene sequence. The purified protein exhibits glutaminase activity of 0.02% the normal turnover, and NH3 can replace glutamine as a nitrogen donor with a Km = 1 M and a turnover of 3 min-1 (2% glutamine turnover). The enzyme forms an isolable (1:1) complex with glutamine: t1/2 is 22 min at 4 degrees C. This isolated complex is not chemically competent to complete turnover when FGAR and ATP are added, demonstrating that ammonia and glutamine are not covalently bound as a thiohemiaminal available to complete the chemical conversion to FGAM. hydroxylamine trapping experiments indicate that glutamine is bound covalently to the enzyme as a thiol ester. Initial velocity and dead-end inhibition kinetic studies on FGAM synthetase are most consistent with a sequential mechanism in which glutamine binds followed by rapid equilibrium binding of MgATP and then FGAR. Incubation of [18O]FGAR with enzyme, ATP, and glutamine results in quantitative transfer of the 18O to Pi.     

Expression of organomercurial lyase in eastern cottonwood enhances organomercury resistance

Summary Release of inorganic mercury pollutants into shallow aquatic environments has resulted in the bacterial production of a more toxic organic mercury species, methylmercury. The bacterial organomercurial lyase (MerB) catalyses the protonolysis of the carbon-mercury bond and releases Hg(II), a less toxic, non-biomagnified form of mercury. Our objective was to engineer eastern cottonwood (Populus deltoides), a fast-growing tree adapted to growth in riparian environments, with the merB gene to explore its potential for phytoremediation of mercury. We produced multiple eastern cottonwood clones expressing a modified bacterial merB gene, confirmed that the gene was expressed in the transclones and tested the regenerated plants for their ability to tolerate exposure to an organic mercury source, phenylmercuric acetate (PMA), in vitro and in hydroponic culture, compared to wild-type control trees. Transgenic merB plants expressed high levels of MerB protein and showed some evidence of higher resistance to the organic mercury than wild-type plants, producing longer roots under exposure to PMA in vitro, although hydroponic culture results were inconclusive. Our results indicate that in order for merB to be useful in eastern cottonwood trees designed to degrade methylmercury at mercury-contaminated aquatic sites, it will probably need to be combined with other genes such as merA.     

Bacterial citrate lyase

Bacterial citrate lyase, the key enzyme in fermentation of citrate, has interesting structural features. The enzyme is a complex assembled from three non-identical subunits, two having distinct enzymatic activities and one functioning as an acyl-carrier protein. Bacterial citrate lyase,si-citrate synthase and ATP-citrate lyase have similar stereospecificities and show cofactor cross-reactions. On account of these common features, the citrate enzymes are promising markers in the study of evolutionary biology. The occurrence, function, regulation and structure of bacterial citrate lyase are reviewed in this article.     

A stable mercury-containing complex of the organomercurial lyase MerB: catalysis, product release, and direct transfer to MerA

Bacteria isolated from organic mercury-contaminated sites have developed a system of two enzymes that allows them to efficiently convert both ionic and organic mercury compounds to the less toxic elemental mercury. Both enzymes are encoded on the mer operon and require sulfhydryl-bound substrates. The first enzyme is an organomercurial lyase (MerB), and the second enzyme is a mercuric ion reductase (MerA). MerB catalyzes the protonolysis of the carbon-mercury bond, resulting in the formation of a reduced carbon compound and inorganic ionic mercury. Of several mercury-containing MerB complexes that we attempted to prepare, the most stable was a complex consisting of the organomercurial lyase (MerB), a mercuric ion, and a molecule of the MerB inhibitor dithiothreitol (DTT). Nuclear magnetic resonance (NMR) spectroscopy and extended X-ray absorption fine structure spectroscopy of the MerB/Hg/DTT complex have shown that the ligands to the mercuric ion in the complex consist of both sulfurs from the DTT molecule and one cysteine ligand, C96, from the protein. The stability of the MerB/Hg/DTT complex, even in the presence of a large excess of competing cysteine, has been demonstrated by NMR and dialysis. We used an enzyme buffering test to determine that the MerB/Hg/DTT complex acts as a substrate for the mercuric reductase MerA. The observed MerA activity is higher than the expected activity assuming free diffusion of the mercuric ion from MerB to MerA. This suggests that the mercuric ion can be transferred between the two enzymes by a direct transfer mechanism.     

The roles of thiols in the bacterial organomercurial lyase (MerB)

The bacterial plasmid-encoded organomercurial lyase, MerB (EC 4.99.1.2), catalyzes the protonolysis of organomercury compounds yielding Hg(II) and the corresponding protonated hydrocarbon. A small, soluble protein with no known homologues, MerB is widely distributed among eubacteria in three phylogenetically distinct subfamilies whose most prominent motif includes three conserved cysteine residues. We found that the 212-residue MerB encoded by plasmid R831b is a cytosolic enzyme, consistent with its high thiol requirement in vitro. MerB is inhibited by the nonphysiological dithiol DTT but uses the physiological thiols, glutathione and cysteine, equally well. Highly conserved Cys96 and Cys159 are essential for activity, whereas weakly conserved Cys160 is not. Proteins mutant in highly conserved Cys117 are insoluble. All MerB cysteines are DTNB-reactive in native and denatured states except Cys117, which fails to react with DTNB in the native form, suggesting it is buried. Mass spectrometric analysis of trypsin fragments of reduced proteins treated with N-ethylmaleimide or iodoacetamide revealed that all cysteines form covalent adducts and remain covalently modifiable even when exposed to 1:1 PHMB prior to treatment with NEM or IAM. Stable PHMB adducts were also observed on all cysteines in mutant proteins, suggesting rapid exchange of PHMB among the remaining protein thiols. However, PHMB exposure of reduced wild-type MerB yielded only Hg adducts on the Cys159/Cys160 peptide, suggesting a trapped reaction intermediate. Using HPLC to follow release of benzoic acid from PHMB, we confirmed that fully reduced wild-type MerB and mutant C160S can carry out a single protonolysis without exogenous thiols. On the basis of the foregoing we refine the previously proposed S(E)2 mechanism for protonolysis by MerB.     

Bacterial growth inhibition by overproduction of protein

Multicopy plasmids that have been engineered to produce large quantitites of a single gratuitous (non-functional, non-toxic) protein are often problematic. When fully induced, these engineered constructions produce very sick bacteria. The reasons for this may be found in the physiology of wild-type laboratory strains that have been selected to grow at maximum rates with optimal quantities of their proteins. Such bacteria apparently experience the accumulation of gratuitous proteins as an internal shift down and they respond to this with a starvation response. Unlike the shift down associated with a change of growth media, the production of large quantities of gratuitous protein is not associated with a new pre-programmed steady-state of balanced growth. Consequently, the starvation response continues until the bacteria commit suicide by, among other things, destroying their ribosomes.     

Bacterial alginate lyase gene: Nucleotide sequence and molecular route for generation of alginate lyase species

A bacterium (strain A1) isolated from a ditch synthesized three types of intracellular alginate lyases: A1-I (molecular weight [M.W.] 60,000), A1-II-2 (M.W. 25,000) and A1-III (M.W. 38,000). The nucleotide sequence of the gene for A1-I lyase, which has been cloned in Escherichia coli DH1 was determined. The open reading frame of the gene encoded 622 amino acids with a calculated M.W. of 69,153. The N-terminal amino acid sequence of A1-I lyase purified from strain A1 or E. coli DH1 cells transformed with the A1-I lyase gene was consistent with the deduced sequence from ⁵⁵His to ⁷⁴Ala, indicating that the A1-I lyase was synthesized as a precursor with a M.W. of 69,153 and then processed to a mature form with a M.W. of 63,681. The N-terminal sequence of the first twenty amino acids of A1-III lyase was found to match that of A1-I lyase. The N-terminal sequence of the first twenty amino acids of A1-II-2 lyase was consistent with the deduced amino acid sequence from ⁴¹⁴Ala to ⁴³³Val in the nucleotide sequence of the A1-I lyase gene. These results indicated that the A1-I lyase was further processed to generate A1-II-2 and A1-III lyase species.     

Cholesterol-degrading bacteria: isolation,characterization and bioconversion

Agrobacterium sp. M4, a gram negative, motile, oxidase- and catalase-positive bacterium isolated from 410 colonies from soil was found to degrade cholesterol with high efficiency (within 9 days). The first and most probably the main metabolite of cholesterol degradation was detectable on TLC from the second day of incubation, and it was identified as 4-cholestene-3-one. No substances with cyclopentenoperhydrophenanthrene structure was found under U.V. radiation at 256 and 336nm, or by staining with sulphuric acid after 9 days of incubation. Morphological, cultural and biochemical characteristics of the isolate placed it in the genus Agrobacterium although its urease activity was negative. Further investigation on this newly isolated strain is under way.     

Peptidyl-alpha-hydroxyglycine alpha-amidating lyase. Purification, characterization, and expression

The production of alpha-amidated peptides from their glycine-extended precursors is a two-step process involving the sequential action of two catalytic domains encoded by the bifunctional peptidylglycine alpha-amidating monooxygenase (PAM) precursor. The NH2-terminal third of the PAM precursor contains the first enzyme, peptidylglycine alpha-hydroxylating monooxygenase (PHM), a copper, molecular oxygen, and ascorbate-dependent enzyme. The middle third of the PAM precursor contains the second enzyme, peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL). The COOH-terminal third of the PAM precursor encodes a transmembrane domain and a hydrophilic domain that may form a cytoplasmic tail. Antisera to a peptide within the PAL domain were used to identify a 50-kDa protein as the major form of PAL in bovine neurointermediate pituitary granules. This 50-kDa PAL protein was purified and found to begin at Asp434 of bPAM, indicating that it could arise through endoproteolytic cleavage of the bPAM precursor at Lys432-Lys433. With alpha-N-acetyl-Tyr-Val-alpha-hydroxyglycine as the substrate, PAL exhibits a pH optimum of 5.0; enzymatic activity is inhibited by high concentrations of salt but is relatively resistant to thiol reagents and urea. PAL activity is inhibited by EDTA and restored by a number of divalent metals, including Cd2+, Cu2+, Zn2+, and Ca2+. Kinetic studies using alpha-N-acetyl-Tyr-Val-alpha-hydroxyglycine indicate that PAL has a Km of 38 microM and a turnover number of 220/s. Expression vectors encoding only the soluble PHM domain or the PAM precursor from which the PHM domain had been deleted were constructed. hEK293 cells transfected with the PHM vector exhibited a 10-fold increase in secretion of PHM activity with no PHM activity detectable in control or transfected cells. hEK293 cells transfected with the PAL vector exhibited a 2-fold increase in secretion of PAL activity and a 15-fold increase in cellular PAL activity. Most of the PAL activity produced by the transfected cells remained membrane-associated.     

A snc1 endocytosis mutant: phenotypic analysis and suppression by overproduction of dihydrosphingosine phosphate lyase

The v-SNARE proteins Snc1p and Snc2p are required for fusion of secretory vesicles with the plasma membrane in yeast. Mutation of a methionine-based sorting signal in the cytoplasmic domain of either Sncp inhibits Sncp endocytosis and prevents recycling of Sncp to the Golgi after exocytosis. snc1-M43A mutant yeast have reduced growth and secretion rates and accumulate post-Golgi secretory vesicles and fragmented vacuoles. However, cells continue to grow and secrete for several hours after de novo Snc2-M42A synthesis is repressed. DPL1, the structural gene for dihydrosphingosine phosphate lyase, was selected as a high copy number snc1-M43A suppressor. Because DPL1 also partially suppresses the growth and secretion phenotypes of a snc deletion, we propose that enhanced degradation of dihydrosphingosine-1-phosphate allows an alternative protein to replace Sncp as the secretory vesicle v-SNARE.     

Bacterial carbon-phosphorus lyase: products, rates, and regulation of phosphonic and phosphinic acid metabolism.

Carbon-phosphorus bond cleavage activity, found in bacteria that utilize alkyl- and phenylphosphonic acids, has not yet been obtained in a cell-free system. Given this constraint, a systematic examination of in vivo C-P lyase activity has been conducted to develop insight into the C-P cleavage reaction. Six bacterial strains were obtained by enrichment culture, identified, and characterized with respect to their phosphonic acid substrate specificity. One isolate, Agrobacterium radiobacter, was shown to cleave the carbon-phosphorus bond of a wide range of substrates, including fosfomycin, glyphosate, and dialkyl phosphinic acids. Furthermore, this organism processed vinyl-, propenyl-, and propynylphosphonic acids, a previously uninvestigated group, to ethylene, propene, and propyne, respectively. A determination of product stoichiometries revealed that both C-P bonds of dimethylphosphinic acid are cleaved quantitatively to methane and, furthermore, that the extent of C-P bond cleavage correlated linearly with the specific growth rate for a range of substrates. The broad substrate specificity of Agrobacterium C-P lyase and the comprehensive characterization of the in vivo activity make this an attractive system for further biochemical and mechanistic experiments. In addition, the failure to observe the activity in a group of gram-positive bacteria holds open the possibility that a periplasmic component may be required for in vivo expression of C-P lyase activity.     

Rat alpha-fetoprotein: isolation, characterization and estrogen-binding properties

Rat α-fetoprotein (α-FP) was isolated from amniotic fluid by an immuno-chemical procedure using high capacity immunoadsorbents. The yield was about 75 p. cent of the initial content in α-FP. The isolated α-FP was found pure by electrophoretic and immunochemical criteria. A molecular weight of 72.000 daltons and a sedimentation coefficient of 4.5 S were estimated by SDS-acrylamide-agarose electrophoresis and sucrose gradient centrifugation, respectively. The latter procedure was also used to study the binding activity of α-FP toward several steroids. All the estrogens tested, estrone, estradiol, estriol and diethylstylbestrol, were bound. By equilibrium dialysis, the intrinsic association constant of pure α-FP was 1 × 10⁸M⁻¹ for estrone and 6 × 10⁷M⁻¹ for estradiol. One molecule of estrone and estradiol was bound per molecule of protein. No significant binding was observed with testosterone and progesterone. The specificity of the estrophilic activity of α-FP appears as a characteristic property of this protein.After electrophoresis of pure α-FP in acrylamide-agarose gels of low porosity (11 p. cent of acrylamide monomer), two closely migrating but distinct bands could be demonstrated. Both forms possess estrogen-binding activity and common antigenic properties. The same molecular heterogeneity of α-FP was observed in whole amniotic fluid.     

Testicular macrophages: isolation, characterization and hormonal responsiveness

Macrophages were isolated from rat testes with trypsin treatment and established in culture using a differential attachment technique. The cells were maintained in culture in Medium 199 at 32 degrees C. The cells were then characterized for their ability to express traditional immunological function as well as to secrete lactate under the regulation of various hormones. The results indicate that viable cultures of macrophages were obtained since: 1) the cells stained intensely for nonspecific esterase, 2) they possessed Fc receptors on their cytoplasmic membranes, 3) they were capable of phagocytosing 3H-labeled E. coli and carbon particles, and 4) they were highly resistant to the effects of trypsin to induce detachment from the culture substrate. These cultures were not contaminated with Leydig cells or Sertoli cells since they were negative for 3 beta-hydroxysteroid dehydrogenase and did not secrete androgen-binding protein (ABP). Most importantly, these cells were capable of responding to follicle-stimulating hormone (FSH) in a dose-dependent manner by increasing the secretion of lactate. Maximal stimulation was observed with 1 microgram FSH/ml which resulted in a 2.5-fold increase over control values. Dibutyryl cyclic AMP (dbcAMP) also caused a dose-related increase in lactate production by these cells. Luteinizing hormone (LH), insulin, testosterone or 17 beta-estradiol had no similar effect on lactate production by these cells. Peritoneal macrophages were not responsive to FSH or dbcAMP. These studies demonstrate that a highly enriched population of testicular macrophages can be maintained in culture and express several immunological characteristics traditionally ascribed to macrophages.(ABSTRACT TRUNCATED AT 250 WORDS)     

Cockroach collagen: isolation, biochemical and biophysical characterization

Collagen fibrils from the mesenteric connective sheath of the adult cockroach Periplaneta americana were extracted by enzymatic digestion with pepsin and were purified. Chromatographic studies and sodium dodecylsulfate electrophoresis revealed the presence of a single chain. It was demonstrated that the structure of this collagen could be represented by the formula (alpha)3. The amino acid composition is typical of collagens (one-third glycine, and a high imino acid content) and similar to that of type II. The carbohydrate content was high (8.8%), and the cyanogen bromide pattern was different from that of known collagens. The chains were linked by the stable intermolecular bond dihydroxylysinonorleucine. The banding patterns of the segment-long-spacing crystallites and of the reconstituted fibrils were similar to type I collagen. The molecular weight (Mr 280,000) and length (285 nm) were typical, but the denaturation temperature was high (38.5 degrees C). It was concluded that cockroach mesenteric collagen showed the characteristic features of invertebrate mesodermal collagens, except that of the thermal stability of the triple-helical structure.