scholarly journals Catalytic consequences of experimental evolution: catalysis by a ‘third-generation’ evolvant of the second beta-galactosidase of Escherichia coli, ebgabcde, and by ebgabcd, a ‘second-generation’ evolvant containing two supposedly ‘kinetically silent’ mutations

1995 ◽  
Vol 312 (3) ◽  
pp. 971-977 ◽  
Author(s):  
S Krishnan ◽  
B G Hall ◽  
M L Sinnott
Keyword(s):  
Escherichia Coli ◽  
Transition State ◽  
Large Subunit ◽  
Small Subunit ◽  
Enzyme Hydrolysis ◽  
Kinetic Activity ◽  
Energy Profiles ◽  
High Concentrations ◽  
Hydrolysis Of ◽  
Beta Galactosidase

The kinetics of hydrolysis of a series of synthetic substrates by two experimentally evolved forms (‘evolvants’), ebgabcd and ebgabcde, of the second beta-galactosidase of Escherichia coli have been measured. The ebgabcd enzyme differs from the wild-type (ebgo) enzyme by Asp92-->Asn (a) and Trp977-->Cys (b) changes in the large subunit, as well as two changes hitherto considered to have no kinetic effect, Ser979-->Gly in the large subunit (c) and Glu122-->Gly in the small subunit (d). The enzyme ebgabcde contains in addition a Glu93-->Lys change in the large subunit (e). Comparison of ebgabcd with ebgab [Elliott, K, Sinnott, Smith, Bommuswamy, Guo, Hall and Zhang (1992) Biochem. J. 282, 155-164] indicates that the c and d changes in fact accelerate the hydrolysis of the glycosyl-enzyme intermediate by a factor of 2.5, and also decrease the charge on the aglycone oxygen atom at the first transition state; the charge on the glycone, however, is unaltered [see K, Konstantinidis, Sinnott and Hall (1993) Biochem. J. 291, 15-17]. The e mutation causes a fall in the degalactosylation rate of about a factor of 3, and its occurrence only together with c and d mutations [Hall, Betts and Wootton (1989) Genetics 123, 635-648] suggests that degalactosylation of a hypothetical ebgabe enzyme would be so slow that the enzyme would have no biological advantage over the ancestral ebgab. The transfer products from galactosyl-ebgabcd and galactosyl-ebgabcde to high concentrations to glucose have been measured; the predominant product is allolactose, but significant quantities of lactose are also formed; however, at apparent kinetic saturation of the galactosyl-enzyme, hydrolysis rather than transfer is the preponderant pathway. A knowledge of the rates of enzyme-catalysed exchange of 18O from [1-18O]galactose to water permits the construction of the free-energy profiles for hydrolysis of lactose by begabcd and ebgabcde. As with the other evolvants, changes in the profile away from the rate-determining transition state are essentially random, and there is no correlation between the changes in the free energies of intermediates and of their flanking transition states. We consider the aggregate of our kinetic data on the ebg system to be telling experimental support for the theoretical objections of Pettersson [Pettersson (1992) Eur. J. Biochem. 206, 289-295 and previous papers] to the Albery-Knowles theory of the evolution of enzyme kinetic activity.

scholarly journals Catalysis by the large subunit of the second β-galactosidase of Escherichia coli in the absence of the small subunit

1995 ◽  
Vol 312 (1) ◽  
pp. 281-286 ◽  
Author(s):  
S V Calugaru ◽  
B G Hall ◽  
M L Sinnott
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Large Subunit ◽  
Small Subunit ◽  
Lac Repressor ◽  
High Yield ◽  
Order Of Magnitude ◽  
Kinetic Effects ◽  
Hydrolysis Of ◽  
Enzyme Intermediate

Plasmids containing the ebgAo and ebgAa genes of Escherichia coli under the control of the lac repressor and promoter have been constructed and inserted into Salmonella typhimurium CH3. This system expresses the large subunit of the ebgo and ebga beta-galactosidase in high yield (20-60% of total protein). The large subunits have been purified to homogeneity. As isolated they are tetramers of significant catalytic activity; the N-terminal amino acid residue is Met, but it is not formylated. The kcat. values for a series of aryl galactosides were 6-200-fold reduced from the corresponding values for the holoenzymes. kcat/Km Values for glycosides of acidic aglycones, though, were unchanged, whilst kcat./Km values for galactosides of less acidic aglycones showed a modest (up to 10-fold) decrease. The kcat. values for glycosides of acidic aglycones hydrolysed by ebgo and ebga large subunits were essentially invariant with aglycone pK, suggesting that hydrolysis of the galactosyl-enzyme intermediate had become rate-determining for these substrates. Rate-determining hydrolysis of the glycosyl-enzyme intermediate was confirmed by pre-steady-state measurements and nucleophilic competition with methanol. Absence of the small subunit was thus estimated to cause a 200-fold decrease in degalactosylation rate for ebgo and a 20-fold one for ebga. beta 1g(V/K) values of -0.57 +/- 0.08 for ebgo and -0.54 +/- 0.08 for ebga isolated subunits were significantly more negative than for holoenzymes. It is suggested that the small subunit is associated with the optimal positioning of the electrophilic Mg2+ ions in these enzymes. Use of PCR in the construction of the plasmid also inadvertently led to the production of psi ebgo large subunit in which there was a PCR-introduced Leu9-->His change. Values of kcat. for aryl galactosides, calculated on the assumption that the psi ebgo large subunit, like the ebgo and ebga large subunits, was 100% active as isolated, were about an order of magnitude lower than for true ebgo large subunit, whilst Km values were similar. The very significant kinetic effect of this inadvertant site-undirected mutagenesis indicates that quite large kinetic effects of amino-acid replacements in enzymes may have no obvious mechanistic significance.

scholarly journals Active-site modification of native and mutant forms of inosine 5′-monophosphate dehydrogenase from Escherichia coli K12

1980 ◽  
Vol 191 (2) ◽  
pp. 533-541 ◽  
Author(s):  
Harry J. Gilbert ◽  
William T. Drabble
Keyword(s):  
Escherichia Coli ◽  
Binding Site ◽  
Enzyme Inactivation ◽  
Enzyme Hydrolysis ◽  
Thiol Groups ◽  
Imp Dehydrogenase ◽  
Nitrobenzoic Acid ◽  
Saturation Kinetics ◽  
Mutant Forms ◽  
Hydrolysis Of

IMP dehydrogenase of Escherichia coli was irreversibly inactivated by Cl-IMP (6-chloro-9-β-d-ribofuranosylpurine 5′-phosphate, 6-chloropurine ribotide). The inactivation reaction showed saturation kinetics. 6-Chloropurine riboside did not inactivate the enzyme. Inactivation by Cl-IMP was retarded by ligands that bind at the IMP-binding site. Their effectiveness was IMP>XMP>GMP»AMP. NAD+ did not protect the enzyme from modification. Inactivation of IMP dehydrogenase was accompanied by a change in λmax. of Cl-IMP from 263 to 290nm, indicating formation of a 6-alkylmercaptopurine nucleotide. The spectrum of 6-chloropurine riboside was not changed by IMP dehydrogenase. With excess Cl-IMP the increase in A290 with time was first-order. Thus it appears that Cl-IMP reacts with only one species of thiol at the IMP-binding site of the enzyme: 2–3mol of Cl-IMP were bound per mol of IMP dehydrogenase tetramer. Of ten mutant enzymes from guaB strains, six reacted with Cl-IMP at a rate similar to that for the native enzyme. The interaction was retarded by IMP. None of the mutant enzymes reacted with 6-chloropurine riboside. 5,5′-Dithiobis-(2-nitrobenzoic acid), iodoacetate, iodoacetamide and methyl methanethiosulphonate also inactivated IMP dehydrogenase. Reduced glutathione re-activated the methanethiolated enzyme, and 2-mercaptoethanol re-activated the enzyme modified by Cl-IMP. IMP did not affect the rate of re-activation of methanethiolated enzyme. Protective modification indicates that Cl-IMP, methyl methanethiosulphonate and iodoacetamide react with the same thiol groups in the enzyme. This is also suggested by the low incorporation of iodo[14C]acetamide into Cl-IMP-modified enzyme. Hydrolysis of enzyme inactivated by iodo[14C]acetamide revealed radioactivity only in S-carboxymethylcysteine. The use of Cl-IMP as a probe for the IMP-binding site of enzymes from guaB mutants is discussed, together with the possible function of the essential thiol groups.

scholarly journals Glutathione-Dependent Conversion ofN-Ethylmaleimide to the Maleamic Acid by Escherichia coli: an Intracellular Detoxification Process

2000 ◽  
Vol 66 (4) ◽  
pp. 1393-1399 ◽  
Author(s):  
D. McLaggan ◽  
H. Rufino ◽  
M. Jaspars ◽  
I. R. Booth
Keyword(s):  
Escherichia Coli ◽  
Time Course ◽  
E Coli ◽  
Transient Activation ◽  
Low Concentrations ◽  
Maleamic Acid ◽  
High Concentrations ◽  
Hydrolysis Of ◽  
Strong Activator ◽  
Detoxification Process

ABSTRACT The electrophile N-ethylmaleimide (NEM) elicits rapid K+ efflux from Escherichia coli cells consequent upon reaction with cytoplasmic glutathione to form an adduct, N-ethylsuccinimido-S-glutathione (ESG) that is a strong activator of the KefB and KefC glutathione-gated K+ efflux systems. The fate of the ESG has not previously been investigated. In this report we demonstrate that NEM andN-phenylmaleimide (NPM) are rapidly detoxified by E. coli. The detoxification occurs through the formation of the glutathione adduct of NEM or NPM, followed by the hydrolysis of the imide bond after which N-substituted maleamic acids are released. N-Ethylmaleamic acid is not toxic to E. coli cells even at high concentrations. The glutathione adducts are not released from cells, and this allows glutathione to be recycled in the cytoplasm. The detoxification is independent of new protein synthesis and NAD+-dependent dehydrogenase activity and entirely dependent upon glutathione. The time course of the detoxification of low concentrations of NEM parallels the transient activation of the KefB and KefC glutathione-gated K+ efflux systems.

scholarly journals Changes in plasma concentration of flavonoids after ingestion of a flavonoid-rich meal prepared with basic foodstuffs

2019 ◽  
Vol 9 (9) ◽  
pp. 558
Author(s):  
Ryo Mannen ◽  
Michiko T Yasuda ◽  
Ayami Sano ◽  
Toshinao Goda ◽  
Kayoko Shimoi ◽  
...  
Keyword(s):  
Antioxidant Activity ◽  
Plasma Concentrations ◽  
Enzyme Hydrolysis ◽  
Single Type ◽  
Flavonoid Content ◽  
Urinary Recovery ◽  
The Third ◽  
High Concentrations ◽  
Habitual Intake ◽  
Hydrolysis Of

Background: As flavonoids have a variety of functions, such as antioxidant activity, there is growing interest in the development of flavonoid supplements. However, there have been reports of DNA damage due to exposure to flavonoids at high concentrations in rats, which could suggest that a habitual intake of flavonoid supplements may cause toxicity. Therefore, we considered that ingesting flavonoids from a typical meal combined basic foodstuffs are safe because of unlikely to result high concentrations like supplements, and focused on the intake of flavonoids from a typical meal. Thus, this study investigated the absorption of flavonoids in humans after the consumption of a typical meal. Methods: On the first 2 days of the study, seven healthy volunteers were provided with low-flavonoid meals (flavonoid content below the detection limit by HPLC: less than 0.24 mg/meal) three times a day as a washout. A flavonoid-rich meal (40.44 ± 1.49 mg/meal) was then provided for breakfast on the third day. Blood was collected from all volunteers 0, 2, 3, 7, 8, and 9 h after the flavonoid-rich meal was consumed. After enzyme hydrolysis of the plasma, the plasma concentrations of flavonoids aglycone of quercetin, daidzein and genistein were measured using LC-MS. Urine was also collected and pooled 24 h after the flavonoid-rich meal was consumed. Thereafter, the urine was treated with enzyme hydrolysis, and the measurement of urinary flavonoids was performed. Results: Plasma flavonoid peaks were observed 8 h after consumption of the flavonoid-rich meal (quercetin: 4.29 ± 1.46 μM, daidzein: 0.51 ± 0.41 μM, genistein: 0.91 ± 0.73 μM). Furthermore, flavonoids were confirmed to be present in plasma even at 9 h after the intake meal. The urinary recovery of flavonoids was 3.43 ± 1.50% for quercetin, 13.87 ± 6.68% for daidzein, and 16.89 ± 11.40% for genistein. Conclusion: These results suggest that consuming a typical meal that combines a variety of basic foodstuffs delays attainment of the plasma flavonoid peak compared with consuming a single type of food or supplements as previously reported. In addition, the flavonoid urinary recovery were also reduced compared with those previously reported. 

scholarly journals Binding energy and catalysis. Fluorinated and deoxygenated glycosides as mechanistic probes of Escherichia coli (lacZ) β-galactosidase

1992 ◽  
Vol 286 (3) ◽  
pp. 721-727 ◽  
Author(s):  
J D McCarter ◽  
M J Adam ◽  
S G Withers
Keyword(s):  
Escherichia Coli ◽  
Transition State ◽  
Kinetic Parameters ◽  
Parent Compound ◽  
Order Rate Constant ◽  
Linear Free Energy Relationship ◽  
Electronic Effects ◽  
Linear Free Energy ◽  
Covalent Intermediate ◽  
Hydrolysis Of

Kinetic parameters for the hydrolysis of a series of deoxy and deoxyfluoro analogues of 2′,4′-dinitrophenyl beta-D-galactopyranoside by Escherichia coli (lacZ) beta-galactosidase have been determined and rates found to be two to nine orders of magnitude lower than that for the parent compound. These large rate reductions result primarily from the loss of transition-state binding interactions due to the replacement of sugar hydroxy groups, and such interactions are estimated to contribute at least 16.7 kJ (4 kcal).mol-1 to binding at the 3, 4 and 6 positions and more than 33.5 kJ (8 kcal).mol-1 at the 2 position. The existence of a linear free-energy relationship between log(kcat./Km) for these compounds and the logarithm of the first-order rate constant for their spontaneous hydrolysis demonstrates that electronic effects are also important and provides direct evidence for oxocarbonium ion character in the enzymic transition state. A covalent intermediate which turns over only extremely slowly (t1/2 = 45 h) accumulates during hydrolysis of the 2-deoxyfluorogalactoside, and kinetic parameters for its formation have been determined. This intermediate is nonetheless catalytically competent, since it re-activates much more rapidly in the presence of the transglycosylation acceptors methanol or glucose, thereby providing support for the notion of a covalent intermediate during hydrolysis of the parent substrates.

scholarly journals Nascent polypeptide chains exit the ribosome in the same relative position in both eucaryotes and procaryotes.

1983 ◽  
Vol 96 (5) ◽  
pp. 1471-1474 ◽  
Author(s):  
C Bernabeu ◽  
E M Tobin ◽  
A Fowler ◽  
I Zabin ◽  
J A Lake
Keyword(s):  
Relative Position ◽  
Large Subunit ◽  
Small Subunit ◽  
Exit Site ◽  
Bisphosphate Carboxylase ◽  
Peptidyl Transfer ◽  
Nascent Chain ◽  
Polypeptide Chains ◽  
Cytoplasmic Ribosomes ◽  
Beta Galactosidase

We located the polypeptide nascent chain as it leaves cytoplasmic ribosomes from the plant Lemna gibba by immune electron microscopy using antibodies against the small subunit of the enzyme ribulose-1,5-bisphosphate carboxylase. Similar studies with Escherichia coli ribosomes, using antibodies directed against the enzyme beta-galactosidase, show that the polypeptide nascent chain emerges in the same relative position in plants and bacteria. The eucaryotic ribosomal exit site is on the large subunit, approximately 75 A from the interface between subunits and nearly 160 A from the central protuberance, the presumed site for peptidyl transfer. This is the first functional site on both the eucaryotic and procaryotic ribosomes to be determined.

scholarly journals Induction of bphA, Encoding Biphenyl Dioxygenase, in Two Polychlorinated Biphenyl-Degrading Bacteria, Psychrotolerant Pseudomonas Strain Cam-1 and MesophilicBurkholderia Strain LB400

2001 ◽  
Vol 67 (6) ◽  
pp. 2669-2676 ◽  
Author(s):  
Emma R. Master ◽  
William W. Mohn
Keyword(s):  
Polychlorinated Biphenyl ◽  
Large Subunit ◽  
Genetic Regulation ◽  
Gene Replacement ◽  
Small Subunit ◽  
Galactosidase Activity ◽  
Biphenyl Dioxygenase ◽  
Degrading Bacteria ◽  
Beta Galactosidase ◽  
In Cells

ABSTRACT We investigated induction of biphenyl dioxygenase in the psychrotolerant polychlorinated biphenyl (PCB) degraderPseudomonas strain Cam-1 and in the mesophilic PCB degraderBurkholderia strain LB400. Using a counterselectable gene replacement vector, we inserted a lacZ-Gmrfusion cassette between chromosomal genes encoding the large subunit (bphA) and small subunit (bphE) of biphenyl dioxygenase in Cam-1 and LB400, generating Cam-10 and LB400-1, respectively. Potential inducers of bphA were added to cell suspensions of Cam-10 and LB400-1 incubated at 30°C, and then beta-galactosidase activity was measured. Biphenyl induced beta-galactosidase activity in Cam-10 to a level approximately six times greater than the basal level in cells incubated with pyruvate. In contrast, the beta-galactosidase activities in LB400-1 incubated with biphenyl and in LB400-1 incubated with pyruvate were indistinguishable. At a concentration of 1 mM, most of the 40 potential inducers tested were inhibitory to induction by biphenyl of beta-galactosidase activity in Cam-10. The exceptions were naphthalene, salicylate, 2-chlorobiphenyl, and 4-chlorobiphenyl, which induced beta-galactosidase activity in Cam-10, although at levels that were no more than 30% of the levels induced by biphenyl. After incubation for 24 h at 7°C, biphenyl induced beta-galactosidase activity in Cam-10 to a level approximately four times greater than the basal level in cells incubated with pyruvate. The constitutive level of beta-galactosidase activity in LB400-1 grown at 15°C was approximately five times less than the level in LB400-1 grown at 30°C. Thus, there are substantial differences in the effects of physical and chemical environmental conditions on genetic regulation of PCB degradation in different bacteria.

scholarly journals Enzyme kinetics of tobacco Rubisco expressed in Escherichia coli varies depending on the small subunit composition

2019 ◽  
Author(s):  
Myat T. Lin ◽  
William D. Stone ◽  
Vishal Chaudhari ◽  
Maureen R. Hanson
Keyword(s):  
Escherichia Coli ◽  
Carbon Fixation ◽  
Large Subunit ◽  
Expression System ◽  
Nuclear Gene ◽  
Small Subunit ◽  
Expression Vectors ◽  
E Coli ◽  
Catalytic Rate ◽  
Chloroplast Stroma

AbstractRubisco catalyzes the first step in carbon fixation and has been a strategic target to improve photosynthetic efficiency. In plants, Rubisco is a complex made up of eight large subunits encoded by a chloroplast gene, rbcL, and eight small subunits expressed from a nuclear gene family and targeted to chloroplast stroma. Biogenesis of Rubisco in plants requires a chaperonin system composed of Cpn60α, Cpn60β and Cpn20, which helps fold the large subunit, and multiple chaperones including RbcX, Raf1, Raf2 and BSD2, which help the dimerization of the folded large subunits and subsequent assembly with the small subunits into L8S8 holoenzymes. A recent study successfully assembled functional Arabidopsis Rubisco in Escherichia coli by co-expressing the two subunits with Arabidopsis chaperonins and chaperones (Aigner et al., 2017). In this study, we modified the expression vectors used in that study and adapted them to express tobacco Rubisco by replacing the Arabidopsis genes with tobacco ones. Next, we surveyed the small subunits present in tobacco, co-expressed each with the large subunit and successfully produced active tobacco enzymes composed of different small subunits in E. coli. These enzymes produced in E. coli have carboxylation kinetics very similar to that of the native tobacco Rubisco. We also produced tobacco Rubisco with a recently discovered trichome small subunit in E. coli and found that it has a higher catalytic rate and a lower CO2 affinity compared to the enzymes with other small subunits. Our improvements in the E. coli Rubisco expression system will allow us to probe features of both the chloroplast and nuclear-encoded subunits of Rubisco that affect its catalytic rate and CO2 specificity.

scholarly journals Purification of Escherichia coli acetohydroxyacid synthase isoenzyme II and reconstitution of active enzyme from its individual pure subunits

1997 ◽  
Vol 327 (3) ◽  
pp. 891-898 ◽  
Author(s):  
M. Craig HILL ◽  
Siew Siew PANG ◽  
G. Ronald DUGGLEBY
Keyword(s):  
Escherichia Coli ◽  
Metal Ion ◽  
Large Subunit ◽  
Plasmid Vector ◽  
Small Subunit ◽  
Enzymic Activity ◽  
Single Step ◽  
Acetohydroxyacid Synthase ◽  
Kinetic Properties ◽  
Fusion Enzyme

The first step in the biosynthesis of branched-chain amino acids is catalysed by acetohydroxyacid synthase (EC 4.1.3.18). The reaction involves the decarboxylation of pyruvate followed by condensation with either a second molecule of pyruvate or with 2-oxobutyrate. The enzyme requires as cofactors thiamine diphosphate, a divalent metal ion and, usually, FAD. In most bacteria the enzyme is a heterotetramer of two large and two small subunits. Escherichia coli contains three active isoenzymes and the present study concerns isoenzyme II, whose large and small subunits are encoded by the ilvG and ilvM genes respectively. Cloning these genes into a plasmid vector and overexpression in E. coli allowed a two-step purification procedure for the native enzyme to be developed. The level of expression is considerably higher from a vector that introduces a 50 residue N-terminal fusion containing an oligohistidine sequence on the large subunit. Purification to homogeneity was achieved in a single step by immobilized-metal-affinity chromatography. The kinetic properties of the native and fusion enzyme are indistinguishable with respect to the substrate pyruvate and the inhibitor chlorsulfuron. The individual subunits were expressed as oligohistidine-tagged fusion proteins and each was purified in a single step. Neither subunit alone has significant enzymic activity but, on mixing, the enzyme is reconstituted. The kinetic properties of the reconstituted enzyme are very similar to those of the fusion enzyme. It is proposed that the reconstitution pathway involves successive, and highly co-operative, binding of two small subunit monomers to a large subunit dimer. None of the cofactors is needed for subunit association although they are necessary for the restoration of enzymic activity.

Structural organization of escherichia coli ribosomes as determined by immuno electron microscopy

1978 ◽  
Vol 36 (2) ◽  
pp. 166-167 ◽  
Author(s):  
G. Stöffler ◽  
R.W. Bald ◽  
J. Dieckhoff ◽  
H. Eckhard ◽  
R. Lührmann ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Escherichia Coli ◽  
Ribosomal Proteins ◽  
Structural Organization ◽  
Three Dimensional ◽  
Ribosomal Subunit ◽  
Spatial Arrangement ◽  
Small Subunit ◽  
Antibody Binding ◽  
Immuno Electron Microscopy

A central step towards an understanding of the structure and function of the Escherichia coli ribosome, a large multicomponent assembly, is the elucidation of the spatial arrangement of its 54 proteins and its three rRNA molecules. The structural organization of ribosomal components has been investigated by a number of experimental approaches. Specific antibodies directed against each of the 54 ribosomal proteins of Escherichia coli have been performed to examine antibody-subunit complexes by electron microscopy. The position of the bound antibody, specific for a particular protein, can be determined; it indicates the location of the corresponding protein on the ribosomal surface.The three-dimensional distribution of each of the 21 small subunit proteins on the ribosomal surface has been determined by immuno electron microscopy: the 21 proteins have been found exposed with altogether 43 antibody binding sites. Each one of 12 proteins showed antibody binding at remote positions on the subunit surface, indicating highly extended conformations of the proteins concerned within the 30S ribosomal subunit; the remaining proteins are, however, not necessarily globular in shape (Fig. 1).

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