Lactobacillus reuteri biofilms formed on porous zein/cellulose scaffolds: Synbiotics to regulate intestinal microbiota

Supplementing probiotics or indigestible carbohydrates is a usual strategy to prevent or revert unhealthy states of the gut by reshaping gut microbiota. One criterion that probiotics are efficacious is the capacity to survive in the gastrointestinal tract. Biofilm is the common growth mode of microorganisms with high tolerances toward harsh environments. Suitable scaffolds are crucial for successful biofilm culture and large-scale production of biofilm-phenotype probiotics. However, the role of scaffolds containing indigestible carbohydrates in biofilm formation has not been studied. In this study, porous zein/cellulose composite scaffolds provided nitrogen sources and carbon sources simultaneously at the solid/liquid interfaces, being beneficial to the biofilm formation of Lactobacillus reuteri. The biofilms showed 2.1-17.4 times higher tolerances in different gastrointestinal conditions. In human fecal fermentation, the biofilms combined with the zein/cellulose composite scaffolds act as the "synbiotics" positively modulating the gut microbiota and the short-chain fatty acids (SCFAs), where biofilms provide probiotics and scaffolds provide prebiotics. The "synbiotics" show a more positive regulation ability than planktonic L. reuteri, presenting potential applications in gut health interventions. These results provide an understanding of the synergistic effects of biofilm-phenotype probiotics and indigestible carbohydrates contained in the "synbiotics" in gut microbiota modulation.

Electrospun Nanofibrous Membranes Accelerate Biofilm Formation and Probiotic Enrichment: Enhanced Tolerances to pH and Antibiotics

Biofilms are the oldest, most successful, and most widely distributed form of microorganism life on earth, existing even in extreme environments. Presently, probiotics in biofilm phenotype are thought as the most advanced fourth-generation probiotics. However, high-efficiency and large-scale biofilm enrichment in an artificial way is difficult. Here, fibrous membranes as probiotic biofilm-enriching materials are studied. Electrospun cellulose acetate nanofibrous membranes with nano-sized fibers show outstanding superiority over fibrous membranes with micron-sized fibers in Lactobacillus paracasei biofilm enrichment. The special 3D structure of electrospun nanofibrous membranes makes other facilitating biofilm formation factors insignificant. With a suitable scaffold/culture medium ratio, nearly 100% of L. paracasei cells exist as biofilm phenotype on the membrane from the very beginning, not planktonic state. L. paracasei biofilms possess a potential for long-term survival and high tolerances toward strong acidic and alkali conditions and antibiotics. RNA sequencing results explain why L. paracasei biofilms possess high tolerances toward harsh environments as compared to planktonic L. paracasei. Electrospun nanofibrous membranes can serve as powerful biofilm-enriching scaffolds for probiotics and other valuable microbes.

Carbon dioxide transport by proteic and facilitated transport membranes

Membrane separation of gases is governed by the permeability of each species across the membrane. The ratio of permeabilities yields the selectivity. Use of certain organic carriers in facilitated transport membranes and the CO2 converting enzyme carbonic anhydrase (CA) in proteic and facilitated transport membranes allows a dramatic increase in CO2 selectivity over other gases. CA has a low Km (9 mM), which we predicted would allow it to scavenge CO2 to very low partial pressures. Our goal was to determine if CA could remove CO2 from an environment at levels of 0.1% or less. Prior measurements of CO2 transport across thin supported liquid membranes showed that addition of CA enhanced CO2 flux by 3- to 100-fold. Proteic films use bifunctional reagents (e.g., glutaraldehyde) to cross-link the enzyme forming a gel. Bovine serum albumin (BSA) is often added for structural stability. Using such a preparation we examined the ability of proteic films to improve CO2 selectivity and to scavenge CO2 from a mixed gas stream. Proof-of-concept results, measured by mass spectrometry, showed a fivefold improvement in CO2 capture rate with maximal improvement at CO2 values of 1% partial pressure difference in the presence of 0 atm absolute difference. At 0.1% CO2 the membrane exhibited a 76% improvement over controls. At 0.3% CO2 the improvement is about threefold. CA proteic membranes exhibit selectivity for CO2 over oxygen and nitrogen in excess of three orders of magnitude. A CA-based proteic or facilitated transport membrane should readily achieve CO2 partial pressures of 0.05% under CELSS conditions. In addition to proteic membranes we are exploring direct immobilization of engineered CA to ultra-high-permeability teflon membranes. Site-directed mutagenesis was used to add functional groups while retaining full enzymatic activity. These results provide a basis for development of far more efficient CO2 capture proteic and facilitated transport membranes with increased selectivity to values closer to 100-fold at 1% CO2. The result will be CO2 selectivity at 0.1% on the order of 400-fold. These results exceed those obtained with other technologies.

A T7 expression vector optimized for site-directed mutagenesis using oligodeoxyribonucleotide cassettes

Site-directed mutagenesis is widely used to examine structure/function relationships in proteins. We have designed a bacterial expression vector series which is optimized for efficient site-directed mutagenesis and subsequent protein synthesis without intervening subcloning steps. The vectors, derived from the T7 expression vectors of Studier and his collaborators [Studier et al., Methods Enzymol. 185 (1990) 60-89], are small and have a bacteriophage f1 origin of replication for production of single-stranded (ss) DNA. Both single-site mutants [using ssDNA and mutating oligodeoxyribonucleotides (oligos)] and cassette mutants (mutagenesis of a short region by inserting double-stranded oligos into unique restriction sites) are rapidly synthesized and expressed with these vectors. Vector construction and use are detailed with examples showing the expression of the sequences encoding human carbonic anhydrases II and III. Production levels of greater than 60 mg of protein per liter of culture have been obtained.

Catalytic enhancement of human carbonic anhydrase III by replacement of phenylalanine-198 with leucine

Carbonic anhydrase III, a cytosolic enzyme found predominantly in skeletal muscle, has a turnover rate for CO2 hydration 500-fold lower and a KI for inhibition by acetazolamide 700-fold higher (at pH 7.2) than those of red cell carbonic anhydrase II. Mutants of human carbonic anhydrase III were made by replacing three residues near the active site with amino acids known to be at the corresponding positions in isozyme II (Lys-64----His, Arg-67----Asn, and Phe-198----Leu). Catalytic properties were measured by stopped-flow spectrophotometry and 18O exchange between CO2 and water using mass spectrometry. The triple mutant of isozyme III had a turnover rate for CO2 hydration 500-fold higher than wild-type carbonic anhydrase III. The binding constants, KI, for sulfonamide inhibitors of the mutants containing Leu-198 were comparable to those of carbonic anhydrase II. The mutations at residues 64, 67, and 198 were catalytically independent; the lowered energy barrier for the triple mutant was the sum of the energy changes for each of the single mutants. Moreover, the triple mutant of isozyme III catalyzed the hydrolysis of 4-nitrophenyl acetate with a specific activity and pH dependence similar to those of isozyme II. Phe-198 is thus a major contributor to the low CO2 hydration activity, the weak binding of acetazolamide, and the low pKa of the zinc-bound water in carbonic anhydrase III. Intramolecular proton transfer involving His-64 was necessary for maximal turnover.

Enhancement of the catalytic properties of human carbonic anhydrase III by site-directed mutagenesis

Among the seven known isozymes of carbonic anhydrase in higher vertebrates, isozyme III is the least efficient in catalytic hydration of CO2 and the least susceptible to inhibition by sulfonamides. We have investigated the role of two basic residues near the active site of human carbonic anhydrase III (HCA III), lysine 64 and arginine 67, to determine whether they can account for some of the unique properties of this isozyme. Site-directed mutagenesis was used to replace these residues with histidine 64 and asparagine 67, the amino acids present at the corresponding positions of HCA II, the most efficient of the carbonic anhydrase isozymes. Catalysis by wild-type HCA III and mutants was determined from the initial velocity of hydration of CO2 at steady state by stopped-flow spectrophotometry and from the exchange of 18O between CO2 and water at chemical equilibrium by mass spectrometry. We have shown that histidine 64 functions as a proton shuttle in carbonic anhydrase by substituting histidine for lysine 64 in HCA III. The enhanced CO2 hydration activity and pH profile of the resulting mutant support this role for histidine 64 in the catalytic mechanism and suggest an approach that may be useful in investigating the mechanistic roles of active-site residues in other isozyme groups. Replacing arginine 67 in HCA III by asparagine enhanced catalysis of CO2 hydration 3-fold compared with that of wild-type HCA III, and the pH profile of the resulting mutant was consistent with a proton transfer role for lysine 64. Neither replacement enhanced the weak inhibition of HCA III by acetazolamide or the catalytic hydrolysis of 4-nitrophenyl acetate.

Enhancement of the catalytic activity of carbonic anhydrase III by phosphates

Phosphate and phosphate-containing buffers of physiological interest such as ATP and 3-phosphoglycerate were found to enhance catalysis by human carbonic anhydrase III (HCA III). Addition of phosphate caused an increase in both the catalyzed rate of hydration of CO2 at steady state measured by stopped-flow spectrophotometry and the exchange of 18O between CO2 and water at chemical equilibrium measured by mass spectrometry. The results are consistent with a mechanism in which phosphate enhances the transfer of protons between zinc-bound water at the active site and solution. Site-directed mutations to replace lysine 64 and arginine 67 in the active-site cavity resulted in greater enhancement by phosphate when compared with wild-type HCA III and showed that these basic residues are not essential as a binding site for phosphate. Phosphate did not enhance catalysis by HCA II.

Circular dichroism and laser Raman spectroscopic analysis of the secondary structure of Cerebratulus lacteus toxin B-IV

The secondary structure of Cerebratulus lacteus toxin B-IV, a neurotoxic polypeptide containing 55 amino acid residues and four disulfide bonds, was experimentally estimated by computer analyses of toxin circular dichroism (CD) and laser Raman spectra. The CD spectrum of the toxin displayed typical alpha-helical peaks at 191, 208, and 222 nm. At neutral pH, the alpha-helix estimates from CD varied between 49 and 55%, when nonrepresentative spectrum analytical methods were used. Analysis of the laser Raman spectrum obtained at a much higher toxin concentration yielded a 78% alpha-helix estimate. Both CD and Raman spectroscopic methods failed to detect any beta-sheet structure. The spectroscopic analyses revealed significantly more alpha-helix and less beta-sheet for toxin B-IV than was predicted from its sequence. To account for the difference between the 49-55% helix estimate from CD spectra and the 78% helix estimate from the Raman spectrum, we postulate that some terminal residues are unfolded at the low toxin concentrations used for CD measurements but form helix at the high toxin concentration used for Raman measurements. Our CD observations showing that Cerebatulus toxin B-IV helix content increases about 15% in trifluoroethanol or at high pH are consistent with this interpretation.

Buffer enhancement of proton transfer in catalysis by human carbonic anhydrase III

Among the isozymes of carbonic anhydrase, isozyme III is the least efficient in the catalysis of the hydration of CO2 and was previously thought to be unaffected by proton transfer from buffers to the active site. We report that buffers of small size, especially imidazole, increase the rate of catalysis by human carbonic anhydrase III (HCA III) of (1) 18O exchange between HCO3- and water measured by membrane-inlet mass spectrometry and (2) the dehydration of HCO3- measured by stopped-flow spectrophotometry. Imidazole enhanced the rate of release of 18O-labeled water from the active site of wild-type carbonic anhydrase III and caused a much greater enhancement, up to 20-fold, for the K64H, R67H, and R67N mutants of this isozyme. Imidazole had no effect on the rate of interconversion of CO2 and HCO3- at chemical equilibrium. Steady-state measurements showed that the addition of imidazole resulted in increases in the turnover number (kcat) for the hydration of CO2 catalyzed by HCA III and for the dehydration of HCO3- catalyzed by R67N HCA III. These results are consistent with the transfer of a proton from the imidazolium cation to the zinc-bound hydroxide at the active site, a step required to regenerate the active form of enzyme in the catalytic cycle. Like isozyme II of carbonic anhydrase, isozyme III can be enhanced in catalytic rate by the presence of small molecule buffers in solution.

Role of histidine 64 in the catalytic mechanism of human carbonic anhydrase II studied with a site-specific mutant

To test the hypothesis that histidine 64 in the active site of human carbonic anhydrase II functions as a proton-transfer group in the catalysis of CO2 hydration, we have studied a site-specific mutant having histidine 64 replaced by alanine, which cannot transfer protons. The steady-state kinetics of CO2 hydration has been measured as well as the exchange of 18O between CO2 and water at chemical equilibrium. The results show that the rate of exchange between CO2 and HCO3- at chemical equilibrium is essentially unaffected by the amino acid substitution at pH greater than 7.0 and slightly decreased in the mutant at pH less than 7.0 (by a factor of 2 at pH 6.0). However, in the absence of buffer the rate of release from the active site of water bearing substrate oxygen is smaller by as much as 20-fold for the mutant as compared to unmodified enzyme. Furthermore, in the unmodified enzyme water release is inhibited by micromolar concentrations of Cu2+ ions, but no such inhibition is observed with the alanine 64 variant. These results suggest that the mutation has specifically affected the rate of proton transfer between the active site and the reaction medium. This kinetic defect in the mutant can be overcome by increasing the concentration of certain buffers, such as imidazole and 1-methylimidazole, but not by others buffers, such as MOPS or HEPES. Similarly, the maximal rate of CO2 hydration at steady state catalyzed by the alanine 64 variant is very low in the presence of MOPS or TAPS buffers but considerably higher in the presence of imidazole derivatives.(ABSTRACT TRUNCATED AT 250 WORDS)

Molecular basis of the oxygen exchange from CO2 catalyzed by carbonic anhydrase III from bovine skeletal muscle

The exchange of 18O from CO2 to H2O in aqueous solution is caused by the hydration-dehydration cycle and is catalyzed by the carbonic anhydrases. In our previous studies of 18O exchange at chemical equilibrium catalyzed by isozymes I and II of carbonic anhydrase, we observed simple first-order depletion of 18O from CO2 with the 18O distribution among the species C18O18O, C16O18O, and C16O16O described by the binomial expansion (i.e., a random distribution of 18O). Using membrane-inlet mass spectrometry, we have measured 18O exchange between CO2 and H2O catalyzed by native zinc-containing and cobalt(II)-substituted carbonic anhydrase III from bovine skeletal muscle near pH 7.5. The distributions of 18O in CO2 deviate from the binomial expansion and are accompanied by biphasic 18O-exchange patterns; moreover, we observed regions in which 18O loss from CO2 was faster than 18O loss from HCO3-. These data are interpreted in terms of a model that includes 18O loss from an enzyme-substrate or intermediate complex. We conclude that more than one 18O can be lost from CO2 per encounter with the active site of isozyme III, a process that requires scrambling of oxygens in a bicarbonate-enzyme complex and cycling between intermediate complexes. This suggests that the rate of dissociation of H2(18)O (or 18OH-) from isozyme III is comparable to or faster than substrate and product dissociation.

Hydrolysis of 4-nitrophenyl acetate catalyzed by carbonic anhydrase III from bovine skeletal muscle

We report three experiments which show that the hydrolysis of 4-nitrophenyl acetate catalyzed by carbonic anhydrase III from bovine skeletal muscle occurs at a site on the enzyme different than the active site for CO2 hydration. This is in contrast with isozymes I and II of carbonic anhydrase for which the sites of 4-nitrophenyl acetate hydrolysis and CO2 hydration are the same. The pH profile of kcat/Km for hydrolysis of 4-nitrophenyl acetate was roughly described by the ionization of a group with pKa 6.5, whereas kcat/Km for CO2 hydration catalyzed by isozyme III was independent of pH in the range of pH 6.0-8.5. The apoenzyme of carbonic anhydrase III, which is inactive in the catalytic hydration of CO2, was found to be as active in the hydrolysis of 4-nitrophenyl acetate as native isozyme III. Concentrations of N-3 and OCN- and the sulfonamides methazolamide and chlorzolamide which inhibited CO2 hydration did not affect catalytic hydrolysis of 4-nitrophenyl acetate by carbonic anhydrase III.

Oxygen-18 Exchange as a Measure of Accessibility of CO(2) and HCO(3) to Carbonic Anhydrase in Chlorella vulgaris (UTEX 263)

We have measured the exchange of (18)O between CO(2) and H(2)O in stirred suspensions of Chlorella vulgaris (UTEX 263) using a membrane inlet to a mass spectrometer. The depletion of (18)O from CO(2) in the fluid outside the cells provides a method to study CO(2) and HCO(3) (-) kinetics in suspensions of algae that contain carbonic anhydrase since (18)O loss to H(2)O is catalyzed inside the cells but not in the external fluid. Low-CO(2) cells of Chlorella vulgaris (grown with air) were added to a solution containing (18)O enriched CO(2) and HCO(3) (-) with 2 to 15 millimolar total inorganic carbon. The observed depletion of (18)O from CO(2) was biphasic and the resulting (18)C content of CO(2) was much less than the (18)O content of HCO(3) (-) in the external solution. Analysis of the slopes showed that the Fick's law rate constant for entry of HCO(3) (-) into the cell was experimentally indistinguishable from zero (bicarbonate impermeable) with an upper limit of 3 x 10(-4) s(-1) due to our experimental errors. The Fick's law rate constant for entry of CO(2) to the sites of intracellular carbonic anhydrase was large, 0.013 per second, but not as great as calculated for no membrane barrier to CO(2) flux (6 per second). The experimental value may be explained by a nonhomogeneous distribution of carbonic anhydrase in the cell (such as membrane-bound enzyme) or by a membrane barrier to CO(2) entry into the cell or both. The CO(2) hydration activity inside the cells was 160 times the uncatalyzed CO(2) hydration rate.

Catalysis by cobalt(II)-substituted carbonic anhydrase II of the exchange of oxygen-18 between CO2 and H2O

We have measured the catalysis by Co(II)-substituted bovine carbonic anhydrase II from red cells of the exchange of 18O between CO2 and H2O using membrane-inlet mass spectrometry. We chose Co(II)-substituted carbonic anhydrase II because the apparent equilibrium dissociation constant of HCO3- and enzyme at pH 7.4, KHCO3-eff approximately equal to 55 mM, was within a practicable range of substrate concentrations for the 18O method. For the native, zinc-containing enzyme KHCO3-eff is close to 500 mM at this pH. The rate constant for the release from the active site of water bearing substrate oxygen kH2O was dependent on the fraction of enzyme that was free, not bound by substrate HCO3- or anions. The pH dependence of kH2O in the pH range 6.0-9.0 can be explained entirely by a rate-limiting, intramolecular proton transfer between cobalt-bound hydroxide and a nearby group, probably His-64. The rate constant for this proton transfer was found to be 7 X 10(5) S-1 for the Co(II)-substituted enzyme and 2 X 10(6) S-1 for the native enzyme. These results are applied to models derived from proton-relaxation enhancement of water exchanging from the inner coordination shell of the cobalt in carbonic anhydrase. The anions iodide, cyanate, and thiocyanate inhibited catalysis of 18O exchange by Co(II)-substituted carbonic anhydrase II in a manner competitive with total substrate (CO2 and HCO3-) at chemical equilibrium and pH 7.4. These results are discussed in terms of observed steady-state inhibition patterns and suggest that there is no significant contribution of a ternary complex between substrate, inhibitor, and enzyme.

Solvent deuterium isotope effects in the catalysis of oxygen-18 exchange by human carbonic anhydrase II

By measuring the rate of exchange at chemical equilibrium of 18O between HCO3- and H2O catalyzed by human carbonic anhydrase II in the absence of buffers, we have determined the rate of release from the enzyme of water bearing substrate oxygen. The ratio of this rate measured in H2O to the rate measured in D2O, the solvent deuterium isotope effect, is between 4 and 9 in the range of pH(D) from 5.8 to 8.0, with a value of 8.0 +/- 0.7 at pH(D) 6.6 (uncorrected pH meter reading). The magnitude of this isotope effect at pH(D) 6.6 has an exponential dependence on the atom fraction of deuterium in solvent water. We conclude that an intramolecular proton transfer between a proton shuttle group on the enzyme and the active site is rate limiting for the release from the enzyme of water bearing substrate oxygen and involves a change in bonding of more than one proton. In contrast, the solvent deuterium isotope effect on the intermolecular proton transfer between the external buffer imidazole and the active site (or proton shuttle group) of the enzyme is small, 2.3 at pH(D) 7.0, as determined from initial velocity experiments. With a rate constant near 9 X 10(8) M-1 s-1, this intermolecular transfer is limited to a significant extent by diffusion processes.

Diffusion-limited exchange of 18O between CO2 and water in red cell suspensions

The loss of 18O from labeled CO2 caused by the exchange of oxygen with water, a process catalyzed by carbonic anhydrase, has been measured in suspensions of rat erythrocytes at pH 7.4 and 25 percent C. The rate of loss of 18O from all CO2 and the rate of loss of 18O from doubly-labeled CO2 are shown to be related to the rate constant for the catalyzed hydration of CO2 inside the cell and a rate constant for the diffusion of CO2 out of the cell. The results show that the diffusion of CO2 out of the cell with a half-time near 2 msec is a slower process than the intracellular, catalytic conversion of CO2 to HCO3- which has a half-time near 0.3 msec. From this information we estimate the gradient of 18O content in CO2 in the red cell during an 18O-exchange experiment. The rate constant for the entry of CO2 into red cells, also obtained from 18O-exchange data, has a value of the same magnitude as that anticipated for the diffusion-controlled rate of encounter between CO2 and red cells. This indication of diffusion-controlled depletion of 18O from Co2 is supported by experiments with a carbonic anhydrase inhibitor which show that carbonic anhydrase does not have a rate-limiting role in the 18O exchange until greater than 80% of the enzyme is inhibited.