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Applied Microbiology and Biotechnology (v.51, #3)

Microbial hydantoinases – industrial enzymes from the origin of life? by C. Syldatk; O. May; J. Altenbuchner; R. Mattes; M. Siemann (pp. 293-309).

Hydantoinases are valuable enzymes for the production of optically pure d- and l-amino acids. They catalyse the reversible hydrolytic ring cleavage of hydantoin or 5′-monosubstituted hydantoins and are therefore classified in the EC nomenclature as cyclic amidases (EC 3.5.2.). In the EC nomenclature, four different hydantoin-cleaving enzymes are described: dihydropyrimidinase (3.5.2.2), allantoinase (EC 3.5.2.5), carboxymethylhydantoinase (EC 3.5.2.4), and N-methylhydantoinase (EC 3.5.2.14). Beside these, other hydantoinases with known metabolic functions, such as imidase and carboxyethylhydantoinase and enzymes with unknown metabolic function, are described in the literature and have not yet been classified. An important question is whether the distinct hydantoinases, which are frequently classified as l-, d-, and non-selective hydantoinases depending on their substrate specificity and stereoselectivity, are related to each other. In order to investigate the evolutionary relationship, amino acid sequence data can be used for a phylogenetic analysis. Although most of these enzymes only share limited sequence homology (identity<15%) and therefore are only distantly related, it can be shown (i) that most of them are members of a broad set of amidases with similarities to ureases and build a protein superfamily, whereas ATP-dependent hydantoinases are not related, (ii) that the urease-related amidases have evolved divergently from a common ancestor and (iii) that they share a metal-binding motif consisting of conserved histidine residues. The difference in enantioselectivity used for the classification of hydantoinases on the basis of their biotechnological value does not reflect their evolutionary relationship, which is to a more diverse group of enzymes than was assumed earlier. This protein superfamily probably has its origin in the prebiotic conditions of the primitive earth.

Influence of microbial concentration on the rheology of non-Newtonian fermentation broths by C. T. Goudar; K. A. Strevett; S. N. Shah (pp. 310-315).

The objective of this study was to quantify the effect of fungal biomass concentration on the rheology of non-Newtonian fermentation systems. Batch fermentations of Penicillium chrysogenum were carried out with glucose as the sole carbon source. The flow behavior of the system was characterized at various fermentation times and was adequately described by the power-law model. The apparent viscosity of the fermentation broth was significantly affected by biomass concentrations in the fermenter. Fermentation broths containing 17.71 g/l biomass as dry weight were characterized by an apparent viscosity of 0.25 Pa s at a shear rate of 50 s⁻¹. Microbial concentration also affected the power-law flow-behavior index and the consistency index. The value of the consistency index ranged from 0.002 Pa s n at a biomass concentration of 0.1 g/l to 6.14 Pa s n at a biomass concentration of 17.71 g/l. The flow-behavior index decreased from an initial value of 1 to a final value of 0.17. Simple empirical correlations have been proposed to quantify the dependence of the power-law parameters on fungal biomass concentration. Experimental data obtained in this study were accurately described by these correlations. The general applicability of these relationships was tested, using previously published rheological data on Aspergillus awamori and Aspergillus niger fermentation broths, and good agreement was seen between experimental data and the predictions from the empirical correlations.

Continuous production of l(+)-lactic acid by Lactobacillus casei in two-stage systems by J. M. Bruno-Bárcena; A. L. Ragout; P. R. Córdoba; F. Siñeriz (pp. 316-324).

A two-stage two-stream chemostat system and a two-stage two-stream immobilized upflow packed-bed reactor system were used for the study of lactic acid production by Lactobacillus casei subsp casei. A mixing ratio of D ₁₂/D ₂= 0.5 (D = dilution rate) resulted in optimum production, making it possible to generate continuously a broth with high lactic acid concentration (48 g l⁻¹) and with a lowered overall content of initial yeast extract (5 g l⁻¹), half the concentration supplied in the one-step process. In the two-stage chemostat system, with the first stage at pH 5.5 and 37 °C and a second stage at pH 6.0, a temperature change from 40 °C to 45 °C in the second stage resulted in a 100% substrate consumption at an overall dilution rate of 0.05 h⁻¹. To increase the cell mass in the system, an adhesive strain of L. casei was used to inoculate two packed-bed reactors, which operated with two mixed feedstock streams at the optimal conditions found above. Lactic acid fermentation started after a lag period of cell growth over foam glass particles. No significant amount of free cells, compared with those adhering to the glass foam, was observed during continuous lactic acid production. The extreme values, 57.5 g l⁻¹ for lactic acid concentration and 9.72 g l⁻¹ h⁻¹ for the volumetric productivity, in upflow packed-bed reactors were higher than those obtained for free cells (48 g l⁻¹ and 2.42 g l⁻¹ h⁻¹) respectively and the highest overall l(+)-lactic acid purity (96.8%) was obtained in the two-chemostat system as compared with the immobilized-cell reactors (93%).

Flux through the tetrahydrodipicolinate succinylase pathway is dispensable for l-lysine production in Corynebacterium glutamicum by C. A. Shaw-Reid; M. M. McCormick; A. J. Sinskey; G. Stephanopoulos (pp. 325-333).

The N-succinyl-ll-diaminopimelate desuccinylase gene (dapE) in the four-step succinylase branch of the l-lysine biosynthetic pathway of Corynebacterium glutamicum was disrupted via marker-exchange mutagenesis to create a mutant strain that uses only the one-step meso-diaminopimelate dehydrogenase branch to overproduce lysine. This mutant strain grew and utilized glucose from minimal medium at the same rate as the parental strain. In addition, the dapE − strain produced lysine at the same rate as its parent strain. Transformation of the parental and dapE − strains with the amplified meso-diaminopimelate dehydrogenase gene (ddh) on a plasmid did not affect lysine production in either strain, despite an eightfold amplification of the activity of the enzyme. These results indicate that the four-step succinylase pathway is dispensable for lysine overproduction in shake-flask culture. In addition, the one-step meso-diaminopimelate dehydrogenase pathway does not limit lysine flux in Corynebacterium under these conditions.

Effects of oxygen on invertase expression in continuous culture of recombinant Saccharomyces cerevisiae containing the SUC2 gene by Y. R. Pyun; J. S. Jo; J. W. Park; H. H. Shin (pp. 334-339).

The yeast SUC2 gene, cloned on a multicopy plasmid pRB58, was used to study the effect of oxygen on the invertase expression of the recombinant Saccharomyces cerevisiae. Glucose repression was not the only factor affecting the invertase expression. The results obtained from the single-stage continuous cultures under microaerobic conditions showed that invertase expression was also strongly dependent on oxygen availability, and moving from anaerobic to aerobic conditions led to a five-fold increase in specific invertase activity. However, the cell yields under anaerobic conditions were quite low compared to those under aerobic conditions. These opposite effects of oxygen on cell growth and gene expression offer a strategy for maximizing invertase productivity by a two-stage continuous culture. The first stage was operated at a low level of glucose, around 100 mg/l, under aerobic conditions in order to obtain a high yield of yeast biomass, and the second stage maintained anaerobic conditions with residual glucose levels of 50 mg/l to derepress and fully induce invertase expression. The two-stage continuous culture resulted in a 2.5-fold increase in invertase productivity over that of a single-stage continuous culture.

Sequencing, expression, and transcription analysis of the Clostridium paraputrificum chiA gene encoding chitinase ChiA by K. Morimoto; S. Karita; T. Kimura; K. Sakka; K. Ohmiya (pp. 340-347).

Immediately (17 bp) upstream of the Clostridium paraputrificum chiB gene [J. Bacteriol. 179: 7306–7314 (1997)], we found another chitinase gene chiA encoding chitinase A (ChiA). The chiA gene consists of an open reading frame of 2496 nucleotides and encodes 832 amino acids with a deduced molecular mass of 92 585 Da. The mature ChiA is a modular enzyme composed of a family-18 catalytic domain responsible for chitinase activity, two cadherin-like domains, and a chitin-binding domain. The domain organization of ChiA is fundamentally identical to that of ChiB and the overall sequence identity between them is 35.4%. ChiA was purified from the periplasm fraction of Escherichia coli harboring the chiA gene. The molecular mass of purified ChiA (89 000 Da), determined by sodium dodecyl sulfate/polyacrylamide gel electrophoresis analysis, was in good agreement with the value (89 119 Da) calculated from the deduced amino acid sequence, excluding the signal peptide. Immunological and N-terminal amino acid sequence analyses revealed that ChiA and ChiB are major chitinases of C. paraputrificum and their production is inducible by ball-milled chitin. Northern blot analysis indicated that the chiA and chiB genes constitute a polycistronic operon. Primer-extension analysis confirmed that the transcription of this operon starts upstream of chiA.

Nucleotide sequences of two contiguous and highly homologous xylanase genes xynA and xynB and characterization of XynA from Clostridium thermocellum by H. Hayashi; M. Takehara; T. Hattori; T. Kimura; S. Karita; K. Sakka; K. Ohmiya (pp. 348-357).

A 5.7-kbp region of the Clostridium thermocellum F1 DNA was sequenced and found to contain two contiguous and highly homologous xylanase genes, xynA and xynB. The xynA gene encoding the xylanase XynA consists of 2049 bp and encodes a protein of 683 amino acids with a molecular mass of 74 511 Da, and the xynB gene encoding the xylanase XynB consists of 1371 bp and encodes a protein of 457 amino acids with a molecular mass of 49 883 Da. XynA is a modular enzyme composed of a typical N-terminal signal peptide and four domains in the following order: a family-11 xylanase domain, a family-VI cellulose-binding domain, a dockerin domain, and a NodB domain. XynB exhibited extremely high overall sequence homology with XynA (identity 96.9%), while lacking the NodB domain present in the latter. These facts suggested that the xynA and xynB genes originated from a common ancestral gene through gene duplication. XynA was purified from a recombinant Escherichia coli strain and characterized. The purified enzyme was highly active toward xylan; the specific activity on oat-spelt xylan was 689 units/mg protein. Immunological and zymogram analyses suggested that XynA and XynB are components of the C. thermocellum F1 cellulosome.

Lactobacillus sanfranciscensis CB1: manganese, oxygen, superoxide dismutase and metabolism by M. De Angelis; M. Gobbetti (pp. 358-363).

The latency phase, growth rate, cell yield and end-products of Lactobacillus sanfranciscensis CB1 were affected by oxygen and the supply of 225 μM Mn²⁺. Mn²⁺ was especially related to the highest substrate consumption. Aerobiosis and Mn²⁺ supply were responsible for the highest superoxide dismutase activity. An auto-inhibitory accumulation of H₂O₂ meant that the survival of air-grown cells supplied with Mn²⁺ rapidly decreased during the stationary phase. As shown by sodium dodecyl sulfate/polyacrylamide gel electrophoresis, Mn²⁺ supply influenced protein expression. As shown by non-denaturating zymograms, Lb. sanfranciscensis CB1 expressed an approximately 12.5-kDa superoxide dismutase, which is probably Mn-dependent. The enzyme was insensitive to H₂O₂ treatment, was not induced by the presence of paraquat under aerobic conditions and was relatively stable at pH 4.0. Sourdoughs that contained high levels of oxygen enhanced cell growth, acidification and acetic acid production by Lb. sanfranciscensis CB1.

Fluorometric observation of viable and dead adhering diatoms using TO-PRO-1 iodide and its application to the estimation of electrochemical treatment by M. Okochi; T. Taguchi; M. Tsuboi; N. Nakamura; T. Matsunaga (pp. 364-369).

A rapid method for the direct measurement of viable and dead adhering diatoms was developed using a fluorescent dye, TO-PRO-1 iodide. By staining the marine diatom, Nitzchia closterium, with TO-PRO-1 iodide, viable and dead cells were identified as red and yellow cells respectively, under an epifluorescence microscope employing blue excitation. Only dead cells were stained with TO-PRO-1 iodide. Viable cells were observed as red because of autofluorescence arising from intracellular chlorophyll, whereas dead cells were observed as yellow because of the fluorescence of TO-PRO-1 iodide. The percentage of TO-PRO-1-iodide-stained was correlated with the percentage of dead cells in N. closterium cells exposed to heat (60 °C, 15 min). Other microalgae containing intracellular chlorophyll could be also distinguished as viable or dead cells by this fluorometric staining method. This method was applied for the assessment of N. closterium cells killed by the electrochemical treatment and used to monitor biofouling populations and their viability directly on the electrode surface. When 1.0 V was applied against a saturated calomel electrode, 99% of the cells attached to graphite electrode were killed in 1 h.

Reversal of the inhibitory effect of surfactants upon germination and growth of a consortium of two strains of Bacillus by P. Ledent; H. Michels; G. Blackman; H. Naveau; S. N. Agathos (pp. 370-374).

Anionic, cationic, amphoteric and non-ionic surfactants inhibited spore germination and subsequent growth of a mixture of two Bacillus strains at surfactant concentrations ranging from 1 ppm to 50 ppm. Germination appeared to be more affected than cell growth by the presence of surfactants, the inhibitory thresholds being largely increased when media were inoculated with vegetative cells. The bacterial species forming the consortium were incapable of growing on liquid and agar-solidified media prepared with non-diluted domestic wastewater. Addition of hydrolases (protease, cellulase, α-amylase and lipase) to the wastewater medium allowed the germination of spores and their vegetative growth.

Inhibition of atrazine degradation by cyanazine and exogenous nitrogen in bacterial isolate M91-3 by N. Gebendinger; M. Radosevich (pp. 375-381).

A variety of s-triazine herbicides and nitrogen fertilizers frequently occur as co-contaminants at pesticide manufacturing and distribution facilities. The degradation of atrazine and cyanazine by the bacterial isolate M91-3 was investigated in washed-cell suspensions and crude cellular extracts. Cyanazine competitively inhibited atrazine degradation. The maximum atrazine degradation rate (V _max) was 41 times higher and the half-saturation constant for the inhibitor (K _i) was 1.3 times higher in the crude cellular extract than in the washed-cell suspension, suggesting that cellular uptake influenced degradation of the s-triazines. Cultures that had received prior exposure to atrazine and simazine exhibited comparable atrazine degradation rates, while cells exposed to cyanazine, propazine, ametryne, cyanuric acid, 2-hydroxyatrazine, biuret, and urea exhibited a lack of atrazine-degradative activity. Growth in the presence of exogenous inorganic nitrogen inhibited subsequent atrazine-degradative activity in washed-cell suspensions, suggesting that regulation of s-triazine and nitrogen metabolism are linked in this bacterial isolate. These findings have significant implications for the environmental fate of s-triazines in agricultural settings since these herbicides are frequently applied to soils receiving N fertilizers. Furthermore, these results suggest that bioremediation of s-triazine-contaminated sites (common at pesticide distribution facilities in the cornbelt) may be inhibited by the presence of N fertilizers that occur as co-contaminants.

Spatial distribution of respiratory activity in Pseudomonas putida 54G biofilms degrading volatile organic compounds (VOC) by S. Villaverde; F. Fernández-Polanco (pp. 382-387).

All over the world, Microbial systems are used to clean soils, waters and air streams that have been contaminated with volatile organic compounds (VOC). Information about the structure and function of the microbes that metabolize these contaminants can be gained by studying these microbial systems. Here we describe the spatial patterns of respiratory activity in Pseudomonas putida 54G aerobic biofilms degrading two VOC, toluene and ethanol. Oxygen concentration profiles within the biofilm were measured using microsensors. These profiles are thought to be most accurate reflection of the structure and function of aerobic microbial biofilms. The degrading process certainly imposed a structural and functional patterns on the microbial biofilm community growing at the expense of the VOC substrate. Cryosectioning coupled with the staining of biofilm samples confirmed a high respiratory activity near the substratum, that decreased towards the biofilm/fluid interface. The accumulation of inactive cells in the outer biofilm layer protects the inner biofilm from high concentrations of toxic compounds and also limits the degradation rate. This stratification phenomenon appeared to be a general pattern for P. putida 54G biofilms degrading VOC.

Activated oxygen species and two extracellular enzymes: laccase and aryl-alcohol oxidase, novel for the lignin-degrading fungus Fusarium proliferatum by V. Regalado; F. Perestelo; A. Rodríguez; A. Carnicero; F. J. Sosa; G. De la Fuente; M. A. Falcón (pp. 388-390).

Laccase, aryl-alcohol oxidase and superoxide radicals were detected in ligninolytic cultures of Fusarium proliferatum. Enzyme activities were present during the secondary metabolism and seen as single protein bands after non-denaturing electrophoresis. In contrast, superoxide radicals were detected during primary growth, correlating with maximal lignin mineralization. Moreover, ligninolysis decreased when scavengers of both superoxide and hydroxyl radicals were added to cultures, indicating that activated oxygen species are involved in lignin degradation.

Effects of Mn²⁺ and NH⁺ ₄ concentrations on laccase and manganese peroxidase production and Amaranth decoloration by Trametes versicolor by J. Swamy; J. A. Ramsay (pp. 391-396).

Extracellular lignin peroxidase (LiP) was not detected during decoloration of the azo dye, Amaranth, by Trametes versicolor. Approximately twice as much laccase and manganese peroxidase (MnP) was produced by decolorizing cultures compared to when no dye was added. At a low Mn²⁺concentration (3 M), N-limited (1.2 mM NH₄ ⁺) cultures decolorized eight successive additions of Amaranth with no visible sorption to the mycelial biomass. At higher Mn²⁺concentrations (200 M), production of MnP increased and that of laccase decreased, but the rate or number of successive Amaranth decolorations was unaffected. There was always a 6-h to 8-h lag prior to decoloration of the first aliquot of Amaranth, regardless of MnP and laccase concentrations. Although nitrogen-rich (12 mM NH₄ ⁺) cultures at an initial concentration of 200 M Mn²⁺ produced high laccase and MnP levels, only three additions of Amaranth were decolorized, and substantial mycelial sorption of the dye occurred. While the results did not preclude roles for MnP and laccase, extracellular MnP and laccase alone were insufficient for decoloration. The cell-free supernatant did not decolorize Amaranth, but the mycelial biomass separated from the whole broth and resuspended in fresh medium did. This indicates the involvement of a mycelial-bound, lignolytic enzyme or a H₂O₂-generating mechanism in the cell wall. Nitrogen limitation was required for the expression of this activity.

Containment of a genetically engineered microorganism during a field bioremediation application by C. Z. Ford; G. S. Sayler; R. S. Burlage (pp. 397-400).

A field release of a genetically engineered microorganism was performed at the Field Lysimeter Site on the Oak Ridge Reservation. Six large lysimeters were filled with soil that had been contaminated with a mixture of naphthalene, phenanthrene, and anthracene. A genetically engineered bacterial strain, Pseudomonas fluorescens HK44, was sprayed onto the surface of the soil during soil loading. This strain contains a fusion between the lux genes of Vibrio fischeri and the promoter for the lower pathway of naphthalene degradation, enabling the strain to become bioluminescent when it is degrading naphthalene. Release of the bacteria outside the lysimeters was monitored, using selective agar plates and one-stage Anderson air samplers. Although approximately 10¹⁴ bacteria were sprayed during the loading process, escape was only detected sporadically; the highest incidence of bacterial escape was found when the relative humidity and wind speed were low.

Long-chain acyl thioesters prepared by solvent-free thioesterification and transthioesterification catalysed by microbial lipases by N. Weber; E. Klein; K. D. Mukherjee (pp. 401-404).

Long-chain acyl thioesters (thio wax esters) have been prepared in high (80% to more than 90%) yields by solvent-free esterification of fatty acids (lauric, myristic, palmitic and stearic acids) with long-chain thiols, such as decane thiol, dodecane thiol, tetradecane thiol and hexadecane thiol, catalysed by lipases from Candida antarctica (Novozym) and Rhizomucor miehei (Lipozyme) in the presence of a 0.4-nm molecular sieve. In the thioesterification reaction Novozym was a more effective biocatalyst than Lipozyme. The extent of thioesterification increased with increasing molar ratio of fatty acid to alkane thiol (1:1 to 3:1) and with temperature (40 °C compared to 60 °C), as well as with the amount of the enzyme preparation and the amount of 0.4-nm molecular sieve. Decreasing the chain length of the alkane thiol from C₁₆ to C₁₀ also increased the extent of thioesterification. Lipase-catalysed solvent-free transthioesterification of fatty acid methyl esters with alkane thiols was less effective for the preparation of acyl thioesters than was thioesterification of fatty acids with alkane thiols. In transthioesterification, Lipozyme was slightly more effective as a biocatalyst than Novozym.

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Applied Microbiology and Biotechnology (v.51, #3)