Purification, cloning, sequencing and over-expression in Escherichia coli of a regioselective aliphatic nitrilase from Acidovorax facilis 72W.

A regioselective aliphatic nitrilase from Acidovorax facilis 72W was purified and characterized, and the corresponding gene was cloned and sequenced. This nitrilase gene was over-expressed in Escherichia coli, generating a microorganism that efficiently and regioselectively catalyzes the conversion of aliphatic dinitriles to cyanocarboxylic acids. The high yields obtained, mild reaction conditions used, and robustness observed make this biocatalyst suitable for industrial applications.

Cloning and nucleotide sequence of amidase gene from Pseudomonas putida.

Amidases are a class of enzymes which convert amides to acids and have potential value in the development of commercial bioprocesses for the production of useful chemicals. A gene encoding an amidase in Pseudomonas putida 5B has been cloned, sequenced, and overexpressed in Escherichia coli. An additional open reading frame (P38K) encoding a putative protein of 38 kDa was found immediately upstream of the amidase gene. This work continues our characterization of a P. putida operon, which now appears to include P38K, amidase, and a stereo-specific nitrile hydratase. This characterization underlies continuing efforts in biocatalyst development.

A stereoselective cobalt-containing nitrile hydratase.

Nitrile hydratase from Pseudomonas putida NRRL-18668 has been purified and characterized. The purified enzyme catalyzes the hydration of 2(S)-(4'-chlorophenyl)-3-methylbutyronitrile at least fifty times faster than that of 2(R)-(4'-chlorophenyl)-3-methylbutyronitrile. This enzyme is a member of the class of nitrile hydratase that contains cobalt. Visible absorption and CD spectra suggest the cobalt exists as a non-corrin low-spin Co3+ ion in a tetragonally-distorted octahedral ligand field. Chemical reduction of the native enzyme results in a species with the EPR signature of a low-spin Co2+ complex. Like the other cobalt-containing nitrile hydratases, this enzyme is relatively stable, maintaining its activity below 35 degrees C, and it shows a broad activity optimum between pH 7.2 and 7.8. The structural genes for this enzyme have been cloned and sequenced. The deduced amino acid sequences for the alpha and beta subunits show 48-63% and 35-41% homology, respectively, to other sequenced nitrile hydratases. In particular, the cysteine residues in the alpha subunit that have been suggested to coordinate the metal ion in the iron-containing nitrile hydratases [Brennan, B. A., Cummings, J. G., Chase, D. B., Turner, I. M., Jr., & Nelson, M. J. (1996) Biochemistry 35, 10068-10077] are conserved in this enzyme, suggesting that this nitrile hydratase, like the enzyme from Rhodococcus rhodochrous J1, is a member of a newly described class of metalloenzymes with Co3+-thiolate ligation [Brennan, B. A., Alms, G., Nelson, M. J., Durney, L. T., & Scarrow, R. C. (1996) J. Am. Chem. Soc. 118, 9194-9195].

Over-production of stereoselective nitrile hydratase from Pseudomonas putida 5B in Escherichia coli: activity requires a novel downstream protein.

The stereoselective nitrile hydratase (NHase) from Pseudomonas putida 5B has been over-produced in Escherichia coli. Maximal enzyme activity requires the co-expression of a novel downstream gene encoding a protein (P14K) of 127 amino acids, which shows no significant homology to any sequences in the protein database. Nitrile hydratase produced in transformed E. coli showed activity as high as 472 units/mg dry cell (sixfold higher than 5B), and retained the stereoselectivity observed in the native organism. Separated from the end of the beta subunit by only 51 bp, P14K appears to be part of an operon that includes the alpha and beta structural genes of nitrile hydratase, and other potential coding sequences.

Purification and Characterization of an Enantioselective Amidase from Pseudomonas chlororaphis B23.

An amidase produced by Pseudomonas chlororaphis B23 was purified and characterized. The purification procedure used included ammonium sulfate precipitation and hydrophobic, anion-exchange, gel filtration, and ceramic hydroxyapatite chromatography steps. This amidase has a native molecular mass of about 105 kDa and is a homodimer whose subunits have a molecular mass of 54 kDa. The enzyme exhibited maximal activity at 50(deg)C and at pH values ranging from 7.0 to 8.6. We found no evidence that metal ions were required, and the enzyme was inhibited by several thiol reagents. This amidase exhibited activity against a broad range of aliphatic and aromatic amides and exhibited enantioselectivity for several aromatic amides, including 2-phenylpropionamide (enantiomeric excess [ee] = 100%), phenylalaninamide (ee = 55%), and 2-(4-chlorophenyl)-3-methylbutyramide (ee = 96%), but not 2-(6-methoxy-2-naphthyl)propionamide (the amide form of naproxen) (ee = 0%). The characteristics of the P. chlororaphis B23 amidase are the same as the characteristics of enantioselective amidases described by Mayaux et al. (J. F. Mayaux, E. Cerbelaud, F. Soubrier, D. Faucher, and D. Petre, J. Bacteriol. 172:6764-6773, 1990; J. F. Mayaux, E. Cerbelaud, F. Soubrier, P. Yeh, F. Blanche, and D. Petre, J. Bacteriol. 173:6694-6704, 1991) and Kobayashi et al. (M. Kobayashi, H. Komeda, T. Nagasawa, M. Nishiyama, S. Horinouchi, T. Beppu, H. Yamada, and S. Shimizu, Eur. J. Biochem. 217:327-336, 1993).

Evidence of hydrolytic route for anaerobic cyanide degradation.

Products observed during anaerobic cyanide transformation are consistent with a hydrolytic pathway (HCN + H2O <--> HCONH2 + H2O <--> HCOOH + NH3). Formate, the most frequently observed product, was generally converted to bicarbonate. Formamide was rapidly hydrolyzed to formate upon exposure to the anaerobic consortium but was not detected as an intermediate of cyanide transformation.

Anaerobic biodegradation of cyanide under methanogenic conditions.

Upflow, anaerobic, fixed-bed, activated charcoal biotreatment columns capable of operating at free cyanide concentrations of greater than 100 mg liter-1 with a hydraulic retention time of less than 48 h were developed. Methanogenesis was maintained under a variety of feed medium conditions which included ethanol, phenol, or methanol as the primary reduced carbon source. Under optimal conditions, greater than 70% of the inflow free cyanide was removed in the first 30% of the column height. Strongly complexed cyanides were resistant to removal. Ammonia was the nitrogen end product of cyanide transformation. In cell material removed from the charcoal columns, [14C]bicarbonate was the major carbon end product of [14C]cyanide transformation.

Bacterial production in freshwater sediments: Cell specific versus system measures.

Estimates of bacterial production based on total trichloroacetic acid (TCA)-precipitable [methyl-(3)H]thymidine incorporation and frequency of dividing cell (FDC) techniques were compared to sediment respiration rates in Lake George, New York. Bacterial growth rates based on thymidine incorporation ranged from 0.024 to 0.41 day(-1), while rates based on FDC ranged from 1.78 to 2.48 day(-1). Respiration rates ranged from 0.11 to 1.8µmol O2·hour(-1)·g dry weight sediment(-1). Thymidine incorporation yielded production estimates which were in reasonable agreement with respiration rates. Production estimates based on FDC were 4- to 190-fold higher than those predicted from respiration rates.

Fundamental procedures for determining ergosterol content of decaying plant material by liquid chromatography.

Portions of published procedures for measurement of ergosterol content of decomposing plants were examined for their influence upon ergosterol yield. Common methods of treatment of plant samples prior to sterol extraction (e.g., oven drying, freezing, lyophilization) led to reduced recoveries of ergosterol (ca. 20 to 80%). The least destructive method was direct placement and storage in methanol. Photoconversion of ergosterol is not likely to cause losses during analysis, but losses are likely if there is insufficient mixing during neutral-lipid partitioning from base-hydrolysis reagents. Homogenization (two times for 2 min) and refluxing (2 h) in methanol were equally effective in extracting ergosterol. Direct extraction in base-hydrolysis reagents was less effective (by ca. 40%).

Use of monodispersed, fluorescently labeled bacteria to estimate in situ protozoan bacterivory.

We have developed a procedure for preparing monodispersed, fluorescently labeled bacteria (FLB), which may be used to measure virtually instantaneous rates of protozoan bacterivory in natural waters. FLB can be prepared both from natural bacterioplankton assemblages and from clonal isolates and can be stored in frozen suspension or freeze-dried without apparent loss of fluorescence intensity. They are not toxic to protozoa and can be metabolized to support bacterivorous protozoan growth rates equal to those on the same strain of unstained, viable bacteria. In experiments comparing uptake of FLB with uptake of fluorescent latex microspheres by protozoan assemblages in a salt marsh tidal creek, we found that both pelagic oligotrichous ciliates and phagotrophic flagellates ingested FLB with a frequency 4- to 10-fold greater than they ingested the microspheres. Consequently, it appears that the use of latex microspheres leads to underestimation of protozoan bacterivory and that the FLB technique is superior for estimating instantaneous rates of in situ protozoan grazing on bacterioplankton.

Thymidine Incorporation by the Microbial Community of Standing Dead Spartina alterniflora.

Thymidine incorporation by the microbial community on standing dead leaves of Spartina alterniflora did not obey many of the assumptions inherent in the use of the technique in planktonic systems. Incorporation rates of [methly-H]thymidine were nonsaturable over a wide concentration range (10 to 10 nM). Owing to metabolism by both fungi and bacteria, a major fraction of the radiolabel (mean, 48%) appeared in protein. Extraction of the radiolabeled macromolecules was inefficient, averaging 8.8%. Based on an empirically derived conversion factor, 4 x 10 cells . mol of thymidine, doubling times ranged from 4 to 69 h for the epiphytic bacterial assemblage.

Influence of rain, tidal wetting and relative humidity on release of carbon dioxide by standing-dead salt-marsh plants.

Dead parts of salt-marsh plants form a considerable fraction of their annual average standing crop. A microbial assemblage living on and in the standing-dead leaves and stems of Spartina alterniflora and Juncus roemerianus responds to saltwater, freshwater or water-vapor wetting by immediately beginning to release CO2. Water-saturated, standing-dead leaves and culms of S. alterniflora release CO2 at steady rates of as much as about 200 and 140 µg CO2-C·g-1 dry·h-1, respectively, at temperatures of 25-30°C, after an initial burst of higher rates. These CO2-release rates are within the range of maximal rates reported for decaying terrestrial litter, and are as high as most rates reported for S. alterniflora decaying under continuously wetted or submerged conditions.

Influences of pH, Temperature, and Moisture on Gaseous Tritium Uptake in Surface Soils.

In South Carolina surface soils, the uptake of gaseous tritium (T(2), HT, or both) showed a broad optimal temperature response from about 20 to 50 degrees C, with the highest rates at 35 to 45 degrees C. The optimal pH was in the range of 4 to 7. Uptake rates declined at the wet and dry extremes in soil moisture content. Inhibition seen upon the addition of hydrogen or carbon monoxide to the soil atmosphere suggested that hydrogenase may be responsible for T(2)-HT uptake in soil. During the period of most rapid recovery in a 36-day incubation of reinoculated, sterilized soil, T(2)-HT uptake rates doubled every 2 to 4 days. Thus, T(2)-HT uptake appears to be biologically mediated. Soil uptake of T(2)-HT was not severely limited by pH, temperature, or moisture in the soils tested. Thus, rapid exchange of gaseous tritium into soil water must be expected and accounted for in modeling the isotope distributions around nuclear facilities.

Bacterial productivity in the water column and sediments of the Georgia (USA) coastal zone: Estimates via direct counting and parallel measurement of thymidine incorporation.

Three methods of estimating bacterial productivity were compared using parallel samples of Atlantic Ocean water (within 0.25-15 km of the Georgia coast). The frequency-of-dividing cells (FDC) method and the [(3)H]thymidine incorporation method gave results which were strongly correlated (r=0.97), but the FDC estimates were always higher (X2 to X7) than the [(3)H]thymidine estimates. Estimates of bacterial productivity ranged from 2-4×10(8) cells·l(-1)·h(-1) at 0.25 km from shore to 1-9×10(7)cells·l(-1)·h(-1) at 15 km. A method involving incubation of 3-µm filtrates and direct counting gave results that could not be easily translated into estimates of bacterial productivity. Application of the FDC method to sediment samples gave high productivity estimates, which could be not reconciled with productivity estimates based on sediment oxygen uptake.

Lytic organisms and photooxidative effects: influence on blue-green algae (cyanobacteria) in lake mendota, wisconsin.

The effects of exposure to high light intensities on blue-green algal (cyanobacterial) populations were examined in Lake Mendota, Wis. The algal populations were shown to be susceptible to inhibition of photosynthetic activity and pigment bleaching as a result of exposure. These effects generally influence only a small percentage of the lake population and thus are probably not important in causing major declines in chlorophyll a. Lytic organisms were shown to increase in numbers in the lake in response to the seasonal development of blue-green algae, reaching values of greater than 1,000 plaque-forming units per ml in midsummer. Both bacteria and protozoa were observed in plaque zones, but it could not be determined whether these lytic organisms had a major role in algal biomass declines.

Decomposition of blue-green algal (cyanobacterial) blooms in lake mendota, wisconsin.

Decomposition of natural populations of Lake Mendota phytoplankton dominated by blue-green algae (cyanobacteria) was monitored by using oxygen uptake and disappearance of chlorophyll, algal volume (fluorescence microscopy), particulate protein, particulate organic carbon, and photosynthetic ability (CO(2) up-take). In some experiments, decomposition of C-labeled axenic cultures of Anabaena sp. was also measured. In addition to decomposition, mineralization of inorganic nitrogen and phosphorus were followed in some experiments. Decomposition could be described as a first-order process, and the rate of decomposition was similar to that found by others using pure cultures of eucaryotic algae. Nitrogen and phosphorus never limited the decomposition process, even when the lake water was severely limited in soluble forms of these nutrients. This suggests that the bacteria responsible for decomposition can obtain all of their key nutrients for growth from the blue-green algal cells. Filtration of lake water through plankton netting that removed up to 90% of the algal biomass usually did not cause a similar decrease in oxygen demand, suggesting that most of the particulate organic matter used for respiration of the decomposing bacteria was in a small-particle fraction. Short-term oxygen demand correlated well with the particulate chlorophyll concentration of the sample, and a relationship was derived that could be used to predict community respiration of the lake from chlorophyll concentration. Kinetic analysis showed that not all analyzed components disappeared at the same rate during the decomposition process. The relative rates of decrease of the measured parameters were as follows: photosynthetic ability > algal volume > particulate chlorophyll > particulate protein. Decomposition of C-labeled Anabaena occurred at similar rates with aerobic epilimnetic water and with anaerobic sediment, but was considerably slower with anaerobic hypolimnetic water. Of the various genera present in the lake, Aphanizomenon and Anabaena were more sensitive to decomposition than was Microcystis. In addition to providing a general picture of the decomposition process, the present work relates to other work on sedimentation to provide a detailed picture of the fate of blue-green algal biomass in a eutrophic lake ecosystem.

Carbon metabolism in model microbial systems from a temperate salt marsh.

The metabolism of a saltwater leachate of 14C-labeled Spartina alterniflora was examined in laboratory systems using mixed, salt marsh microbial communities and, by addition of appropriate antibiotics, communities with bacteria or eukaryotes inhibited. Label uptake was more rapid in the systems with bacteria alone and with the mixed microbial community than with fungi alone. Mineralization of the added label was more extensive in the mixed and bacterial systems, whereas the fungi appear more efficient at converting the label into particulate biomass. Particulate biomass production efficiencies ranged from a high of 0.82 for the fungal system to 0.21 in the mixed community, with the bacterial system giving an intermediate value of 0.54. The presence of protozoa and microcrustaceans in the mixed system appears to account for an increase in the mineralization of the label assimilated. Additional experiments with whole labeled Spartina, a leachate from Spartina, and Spartina after leaching revealed that the seawater-soluble portions of the plants were attacked most rapidly by the microbial community.