Purification and characterization of a deoxyriboendonuclease from Mycobacterium smegmatis

A deoxyriboendonuclease has been purified to near homogeneity from a fast growing mycobacterium species, M. smegmatis and characterized to some extent. The size of enzyme is about 43 kDa as determined by a denaturing gel analysis. It shows optimum activity at 32 degrees C in Tris-HCl buffer (pH 7.2) containing 2.5 mM of MgCl2. Both EDTA and K+ but not Na+ inhibit its activity. Evidences show that the enzyme is not a restriction endonuclease but catalyzes the endonucleolytic cleavage of both the double- as well as the single-strand DNA non-specifically. It has been shown that the cleavage by this enzyme generates DNA fragments carrying phosphate groups at 5' ends and hydroxyl group at the 3' ends, respectively. Analysis reveals that no endonuclease having size and property identical to our deoxyriboendonuclease had been purified from M. smegmatis before. The property of our enzymes closely matches with the deoxyriboendonucleases purified from diverse sources including bacteria.     

Purification and characterization of dihydrofolate reductase from wild-type and trimethoprim-resistant Mycobacterium smegmatis

Dihydrofolate reductase (DHFR) from extracts of Mycobacterium smegmatis strain mc2(6) and trimethoprim-resistant mutant mc2(26) was purified to homogeneity. In crude extracts, the specific activity of the enzyme from the trimethoprim resistant strain was comparable to that from the sensitive strain. The DHFR from both sources was purified using affinity chromatography on MTX-Sepharose followed by Mono Q FPLC. The enzyme has an apparent molecular mass of 23 kDa from gel filtration on Sephadex G-100 and from SDS-PAGE. Amino terminal sequence analysis showed homology with DHFRs from a subset of other gram-positive organisms. The purified enzyme from the trimethoprim-sensitive organism exhibited Km values for H2folate and NADPH of 0.68 +/- 0.2 microM and 21 +/- 4 microM, respectively. The Km values for H2folate and NADPH for the enzyme from the drug-resistant organism were 1.8 +/- 0.4 microM and 5.3 +/- 1.5 microM, respectively. A kcat of 4.5 sec-1 was determined for the DHFR from both sources. The enzyme from both sources was competitively inhibited by pyrimethamine and trimethoprim. The Ki value of trimethoprim, for the enzyme from the drug-resistant organism was about six-fold higher than for the enzyme from drug-sensitive strain. Our data suggest that mutation of DHFR contributes to trimethoprim resistance in the mc2(26) strain of M. smegmatis.     

Purification and partial characterization of a penicillin-binding protein from Mycobacterium smegmatis.

Penicillin-binding proteins (PBPs), although characterized from several organisms, have so far not been studied in mycobacteria. The present study is the first characterization of a PBP from Mycobacterium smegmatis. The PBP was purified by solubilization of the membranes with Triton X-100 and successive chromatography of the solubilized proteins on ampicillin-linked CH Sepharose 4B and DE-52. The purified PBP (M(r), 49,500) catalyzed a model transpeptidase reaction with the tripeptide acetyl2-L-Lys-D-Ala-D-Ala as the substrate and Gly-Gly as the acceptor. The transpeptidase activity was inhibited by 50% at a benzylpenicillin concentration of 1.8 x 10(-7) M, which was similar to the concentration (1.1 x 10(-7) M) of benzylpenicillin required to saturate to 50% this PBP. Of several antibiotics tested, the concentration of antibiotic required to inhibit [35S]penicillin binding by 90% was found to be the lowest for cefoxitin and Sch 34343.     

Acetyl-CoA-dependent elongation of fatty acids in Mycobacterium smegmatis.

An enzyme system of Mycobacterium smegmatis catalyzing the elongation of medium-chain fatty acids with acetyl-CoA was obtained free from de novo fatty acid synthetase by ammonium sulfate fractionation. The system was resolved by gel filtration and DEAE-cellulose chromatography into three fractions, all of which were required for reconstitution of the elongation activity. The three fractions were highly purified enoyl-CoA hydratase, highly purified 3-hydroxyacyl-CoA dehydrogenase, and a fraction containing both enoyl-CoA reductase and thiolase. The reconstituted system was avidin-insenstive, required NADH as a sole hydrogen donor, and was sensitive to pCMB, but not to N-ethylmaleimide or monoiodoacetate. Decanoyl-CoA and octanoyl-CoA were the best primers for the elongation system. When decanoyl-CoA was used as the primer, the major product was found to be a lauroyl derivative (probably lauroyl-CoA). Evidence was obtained suggesting that acyl-CoA dehydrogenase, catalyzing the first step of beta-oxidation, was not functional in the elongation system.     

Purification and characterization of 3-oxoacyl-CoA synthase of Mycobacterium smegmatis

3-Oxoacyl-CoA synthase, that condenses malonyl-CoA to other acyl-CoAs and takes part in the malonyl-CoA-dependent, acyl carrier protein (ACP)-non-requiring fatty acid elongation system ("fatty acid elongation system II or elongation system II" (Kikuchi, S. & Kusaka, T. (1982) J. Biochem. 92, 839-844)), was purified to homogeneity for the first time from the crude extract of Mycobacterium smegmatis by column-chromatographies. The molecular weight of this enzyme was estimated to be around 64,000 by Sephacryl S-300 gel filtration and 59,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzymic product from malonyl-CoA and stearoyl-CoA was identified as 3-oxoeicosanoyl-CoA by mass-spectrometry. Km values of the enzyme for malonyl-CoA and stearoyl-CoA were 41.7 microM and 52.6 microM, respectively. The enzyme was more active toward acyl-CoAs having acyl-carbon-numbers of 18 or more, either saturated or monounsaturated, than those with below 18. Cerulenin, a specific inhibitor of 3-oxoacyl-ACP synthase [EC 2.3.1.41], had no effect on this enzyme but iodoacetamide and N-ethylmaleimide (NEM) showed inhibitory effects.     

Purification and characterization of 3-hydroxyacyl-CoA dehydrogenase of Mycobacterium smegmatis

3-Hydroxyacyl-CoA dehydrogenase [EC 1.1.1.35] was purified 100-fold to homogeneity from crude extracts of Mycobacterium smegmatis, using ammonium sulfate fractionation, gel filtration, and chromatography on DEAE-cellulose, hydroxyapatite, and NAD-Sepharose 4B columns. Its molecular weight was estimated to be 50,300 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. NADH acted twelve times more efficiently than NADPH as an electron donor for the reduction of 3-ketoacyl-CoA, and there was strict substrate stereospecificity (L form) in the oxidation of 3-hydroxyacyl-CoA. The pH optimum depended upon the direction of reaction, i.e., 6.0 for the oxidation of NADH and 9--10 for the reduction of NAD. The Km values for different thioesters of acetoacetate, i.e., esters of CoA, pantetheine, and acetyl-cysteamine were determined to be 0.036, 1.19, and 44.4 mM, respectively. Antibodies raised against the dehydrogenase of M. smegmatis strongly inhibited the enzyme activity, but did not affect the corresponding dehydrogenase of pig heart. The antibodies were found to inhibit the acetyl-CoA dependent elongation of fatty acids by the crude extract of M. smegmatis. These findings, together with those on the reconstitution of the elongation activity reported previously (Shimakata, T., Fujita, Y., & Kusaka, T. (1977) J. Biochem. 82, 725-732) indicate that 3-hydroxyacyl-CoA dehydrogenase is involved in the acetyl-CoA dependent elongation of fatty acids in M. smegmatis.     

Purification and characterization of a novel mycolic acid exchange enzyme from Mycobacterium smegmatis

We have isolated and purified to homogeneity an alpha,alpha'-trehalose 6-monomycolate:alpha,alpha'-trehalose mycolyltransferase (trehalose mycolyltransferase) from Mycobacterium smegmatis that catalyzes the exchange of a mycolyl group between trehalose, trehalose 6-monomycolate (TM), and trehalose 6,6'-dimycolate (TD). This enzyme was prominent in M. smegmatis and it catalyzed the following reactions. TM + [14C]trehalose in equilibrium [14C]TM + trehalose [14C]TM + TM in equilibrium [14C]TD + trehalose This enzyme was purified by (i) ammonium sulfate fractionation, (ii) QAE-Sephadex A-50 column chromatography, (iii) gel filtration on a Sephadex G-75 column, and (iv) SP-Sephadex C-50 column chromatography. The purified protein yielded a single band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and its molecular weight was estimated to be 25,000. This enzyme was a glycoprotein, had no cofactor requirement, and was highly specific for alpha,alpha'-trehalose as the mycolate acceptor. It was less specific for the acyl donor group since the palmitoyl group in trehalose 6-monopalmitate was easily exchangeable. There was no TM acylhydrolase activity in the purified enzyme, suggesting that it is probably associated with the anabolic pathway of mycolic acid metabolism. We postulate the formation of a mycolyl-enzyme intermediate in this reaction. Such an intermediate could play a central role in the transfer of mycolic acid to form the prominent cell wall components of mycobacterial TD and possibly murein-arabinogalactan-mycolate.     

Purification and characterization of the tween-hydrolyzing esterase of Mycobacterium smegmatis.

An esterase hydrolyzing Tween 80 (polyoxyethylene sorbitan monooleate) was purified from sonicated cell lysates of Mycobacterium smegmatis ATCC 14468 by DEAE-cellulose, Sephadex G-150, phenyl Sepharose, and diethyl-(2-hydroxypropyl) aminoethyl column chromatography and by subsequent preparative polyacrylamide gel electrophoresis. The molecular weight was estimated to be 36,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and 41,000 by gel filtration on a Sephadex G-150 column. The esterase contained a single polypeptide. The esterase was stable to heat treatment at 100 degrees C and to a wide range of pH. The temperature and pH optima for the hydrolysis of Tween 80 were 50 degrees C and 8.3, respectively. The esterase had a narrow substrate specificity; it exhibited a high activity only on compounds having both polyoxyethylene and fatty acyl moieties, such as Tweens. Monoacylglyceride was hydrolyzed more slowly by this esterase and this enzyme exhibited a nonspecific esterase activity on p-nitrophenyl acyl esters, especially those having short chain acyl moieties. The Km and Vmax were 19.2 mM and 1,670 mumol/min per mg of protein for Tween 20, 6.6 mM and 278 mumol/min per mg of protein for Tween 80, and 0.25 mM and 196 mumol/min per mg of protein for p-nitrophenyl acetate, respectively. Observations of the effects of various chemical modifications on the activity of the esterase indicated that tyrosine, histidine, arginine, and methionine (with tryptophan) residues may be active amino acids which play important roles in the expression of Tween 80-hydrolyzing activity of the enzyme.     

Purification and properties of aspartate transcarbamylase from Mycobacterium smegmatis

Aspartate transcarbamylase (carbamoyl-phosphate: L-aspartate carbamoyltransferase, EC 2.1.3.2) has been purified from Mycobacterium smegmatis TMC 1546 using streptomycin sulphate precipitation, ammonium sulphate precipitation, DE-52 chromatography, second ammonium sulphate precipitation, Sephadex G-200 gel filtration, and aspartate-linked CNBr-activated Sepharose 4B affinity chromatography in successive order. The enzyme was purified 231.6-fold, and the preparation was found to be homogeneous on column chromatography and polyacrylamide gel electrophoresis. The purified enzyme had a molecular weight of 246,000 and was composed of two asymmetrical subunits. The kinetic and regulatory properties of aspartate transcarbamylase from M. smegmatis were also studied. The enzyme was found to be an allosteric in nature with carbamyl phosphate showing positive cooperativity and UMP exhibiting a negative cooperativity. CTP was found to be the most potent inhibitor among nucleotides. Phosphate acted as a non-competitive product inhibitor with respect to aspartate. Succinate and maleate exerted a competitive inhibition when aspartate was the variable substrate.     

Purification and properties of pyruvate kinase from Mycobacterium smegmatis

Pyruvate kinase (ATP:pyruvate 2-O-phosphotransferase, EC 2.7.1.40) from Mycobacterium smegmatis has been purified to homogeneity through a seven-step procedure with a yield of 16% and specific activity of 220 units/mg protein. The purified enzyme had a molecular weight of 230,700 and was composed of four subunits with identical molecular weights of 57,540. Analysis of amino acid composition revealed a low content of aromatic amino acids. The enzyme exhibited sigmoidal kinetics of varying concentrations of phosphoenolpyruvate, the degree of cooperativity and S_0.5v value for phosphoenolpyruvate being strongly dependent on the pH of the reaction mixture. Among the nucleoside diphosphates acting as substrate for pyruvate kinase, ADP was the best phosphate acceptor, as judged by its lowest K_m value. The enzyme showed an absolute requirement for divalent cations (either Mg²⁺ or Mn²⁺), but monovalent cations were not necessary for activity. Other divalent cations inhibited the Mg²⁺-activated enzyme to varying degrees (Ni²⁺ > Zn²⁺ > Cu²⁺ > Ca²⁺ > Ba²⁺). The differences in the kinetic responses of the enzyme to Mg²⁺ and Mn²⁺ are discussed.     

Purification of a D-mannose isomerase from Mycobacterium smegmatis

An enzyme, d-mannose ketol isomerase, catalyzing the isomerization of d-mannose and d-fructose was purified approximately 60-fold from cells of Mycobacterium smegmatis grown on mannose as the sole carbon source. This enzyme was shown to catalyze the conversion of d-mannose and d-lyxose to ketoses. The ketose produced from mannose was identified as fructose by chemical and chromatographic methods. The reaction was shown to be reversible, the equilibrium ratio of fructose to mannose being approximately 65 to 35. The pH optimum was about 7.5, and the K(m) for mannose was estimated to be 7 x 10(-3)m. Mannose isomerase activity was greatest in cells grown on mannose, whereas cells grown on fructose had about 30% as much activity. Very low levels of activity were detected in cells grown on other substrates. There was an immediate increase in enzyme activity on transfer of cells from nutrient broth to a mannose mineral salts medium.     

Purification and properties of valyl-tRNA synthetase from Mycobacterium smegmatis.

Valyl-tRNA synthetase from Mycobacterium smegmatis has been purified over 1200-fold by conventional techniques as well as affinity chromatography on valyl-aminohexyl Sepharose columns. The purified preparation is homogeneous by electrophoretic and immunologic criteria. The enzyme is a tetramer of approximate molecular weight of 120,000, composed of a single type of subunit. The synthetase exhibited maximal activity between 35--40 degrees C and pH 6.8--7.0. The pure enzyme though stable for several months below 0 degrees C, loses activity completely at 70 degrees C, for 1 min. The enzyme showed normal Michaelis-Menten kinetic behaviour in the total aminoacylation reaction with Km values of 1.25 microM, 0.1 mM and 1.0 microM for valine, ATP and tRNA, respectively, but the kinetic response deviated from the above pattern in the partial (activation) reaction. Based on these findings, the existence of the enzyme in two molecular forms, modulated by substrate concentration has been suggested; of these, only one may be active in the total reaction, while both forms may function in the phophosphate exchange reaction.     

Fructose diphosphate aldolase from Mycobacterium smegmatis. Purification and properties.

Fructose diphosphate aldolase has been purified to homogeneity from Mycobacterium smegmatis. Physicochemical studies showed that the enzyme is a tetramer of molecular weight 158,000. Mycobacterium smegmatis aldolase, though a bacterial enzyme, possesses properties similar to other class I aldolases. Inactivation of the enzyme by sodium borohydride in presence of dihydroxyacetone phosphate suggested the formation of a Schiff-base intermediate.     

Purification and kinetic mechanism of lysyl-tRNA synthetase from Mycobacterium smegmatis SN2

Lysyl-tRNA synthetase [L-lys:tRNAlys ligase (AMP forming) EC:6.1.1.6] has been purified to homogeneity from Mycobacterium smegmatis SN2. The enzyme is a dimer of molecular weight 126,000 and is composed of identical subunits. A detailed analysis of the kinetic mechanism of the lysyl-tRNA synthetase has been carried out. A rapid equilibrium random ter ter mechanism is proposed based on initial velocity and product inhibition studies. There is no evidence for the formation of enzyme-bound lysyl-adenylate. The reverse reaction, studied by the deacylation of lysyl-tRNA, requires the presence of both AMP and PPi. This observation is consistent with the mechanism proposed.     

Isolation and partial characterization of a very long-chain fatty acid desaturation system from the cytosol of Mycobacterium smegmatis

The supernatant fraction after 105,000 X g centrifugation of an extract of sonically disrupted cells of Mycobacterium smegmatis catalyzed the desaturation of lignoceroyl-CoA to a delta15-monounsaturated derivative in the presence of molecular oxygen and NADPH. This desaturation system was separated by ammonium sulfate fractionation, gel filtration, DEAE-cellulose column chromatographies, and affinity column chromatography on immobilized dye, into three components; a NADPH-oxidase, a ferredoxin-containing fraction and a desaturase, all of which were required for the reconstituted desaturation system for lignoceroyl-CoA. This system was inhibited by FMN and ferrous ions but not by KCN. All of these features clearly distinguish this system from the previously known fatty acid desaturation systems of various origins.