It has been shown that Pseudomonas putida GPo1 is able to grow in continuous culture simultaneously limited by ammonium (N source) and octanoate (C source), and concomitantly accumulate poly([R]-3-hydroxyalkanoate) (PHA). Under such growth conditions the material properties of PHA can be fine-tuned if a second PHA precursor substrate is supplied. To determine the range of dual carbon and nitrogen (C, N)-limited growth conditions, tedious chemostat experiments need to be carried out for each carbon source separately. To determine the growth regime, the C/N ratio of the feed (f) to a chemostat was changed in a stepwise manner at a constant dilution rate of 0.3/h. Dual-(C, N)-limited growth was observed between C(f) /N(f) ≤ 6.4 g/g and C(f) /N(f) >9.5 g/g. In the following, we analyzed alternative approaches, using continuous medium gradients at the same dilution rate, that do not require time consuming establishments of steady states. Different dynamic approaches were selected in which the C(f) /N(f) ratio was changed continuously through a convex increase of C(f) , a convex increase of N(f) , or a linear decrease of C(f) (gradients 1, 2, and 3, respectively). In these experiments, the dual-(C, N)-limited growth regime was between 7.2 and 11.0 g/g for gradient 1, 4.3 and 6.9 g/g for gradient 2, and 5.1 and 8.9 g/g for gradient 3. A mathematical equation was developed that compensated a time delay of the gradient that was caused by the wash-in/wash-out effects of the medium feed.

The bacterial production of medium-chain-length polyhydroxyalkanoate (PHA) in continuous two-stage cultivation was investigated. Two chemostats were linked in sequence and Pseudomonas putida GPo1 was supplied with different concentrations of octanoic acid in the first and 10-undecenoic acid in the second reactor. PHA isolated from the second bioreactor was a blend of two copolymers typically consisting of poly(3-hydroxyoctanoate-co-3-hydroxyhexanoate) (PHO) and poly(3-hydroxy-10-undecenoate-co-3-hydroxy-8-nonenoate-co-3-hydroxy-6-heptenoate) (PHUE) with structural (monomeric) purities of 85-95 mol %, indicating simultaneous PHA accumulation and degradation inside the cell. The maximum PHA content was found to be 53.8% of total cell dry weight, which is very high for mcl-PHA.

BACKGROUND:Medium chain length (mcl-) polyhydroxyalkanoates (PHA) are synthesized by many bacteria in the cytoplasm as storage compounds for energy and carbon. The key enzymes for PHA metabolism are PHA polymerase (PhaC) and depolymerase (PhaZ). Little is known of how mcl-PHA accumulation and degradation are controlled. It has been suggested that overall PHA metabolism is regulated by the β-oxidation pathway of which the flux is governed by intracellular ratios of [NADH]/[NAD] and [acetyl-CoA]/[CoA]. Another level of control could relate to modulation of the activities of PhaC and PhaZ. In order to investigate the latter, assays for in vitro activity measurements of PhaC and PhaZ in crude cell extracts are necessary.RESULTS:Two in vitro assays were developed which allow the measurement of PhaC and PhaZ activities in crude cell extracts of Pseudomonas putida U. Using the assays, it was demonstrated that the activity of PhaC decreased 5-fold upon exponential growth on nitrogen limited medium and octanoate. In contrast, the activity of PhaZ increased only 1.5-fold during growth. One reason for the changes in the enzymatic activity of PhaC and PhaZ could relate to a change in interaction with the phasin surface proteins on the PHA granule. SDS-PAGE analysis of isolated PHA granules demonstrated that during growth, the ratio of [phasins]/[PHA] decreased. In addition, it was found that after eliminating phasins (PhaF and PhaI) from the granules PhaC activity decreased further.CONCLUSION:Using the assays developed in this study, we followed the enzymatic activities of PhaC and PhaZ during growth and correlated them to the amount of phasins on the PHA granules. It was found that in P. putida PhaC and PhaZ are concomitantly active, resulting in parallel synthesis and degradation of PHA. Moreover PhaC activity was found to be decreased, whereas PhaZ activity increased during growth. Availability of phasins on PHA granules affected the activity of PhaC.

The regulation of medium-chain-length polyhydroxyalkanoates (mcl-PHA) metabolism in Pseudomonas putida GPo1 was studied by analysis of enzymes bound to PHA granules and enzymes involved in fatty acid oxidation. N-terminal sequencing of granule-bound enzymes revealed the presence of PHA polymerase (PhaC) and PHA depolymerase (PhaZ) and an acyl-CoA synthetase (ACS1), which recently was found to be associated with PHA granules by in vivo study. The acs1 knockout mutant accumulated 30-50% less PHA than its parental strain, confirming the involvement of ACS1 in PHA metabolism. Isolated PHA granules showed both PhaC and PhaZ activities. PhaC activity was found to be sensitive to the ratio of [R-3-hydroxyacyl-CoA]/[CoA] in which free CoA was a mild competitive inhibitor. Fatty acid oxidation was regulated by the [acetyl-CoA]/[CoA] and [NADH]/[NAD] ratios, with high ratios resulting in accumulation and low ratios leading to rapid oxidation of 3-hydroxyacyl-CoA. These results suggest that PHA metabolism is likely to be controlled by the [acetyl-CoA]/[CoA] and [NADH]/[NAD] ratios. The physiological roles of simultaneous PHA accumulation and degradation are also discussed.

Polyhydroxyalkanoates (PHA) are synthesized by many bacteria in the cytoplasm as storage compounds for energy and carbon. The key enzymes for PHA biosynthesis are PHA polymerases, which catalyze the covalent linkage of 3-hydroxyacyl coenzymeA thioesters by transesterification with concomitant release of CoA. Pseudomonas putida GPo1 and many other Pseudomonas species contain two different class II polymerases, encoded by phaC1 and phaC2. Although numerous studies have been carried out on PHA polymerases and they are well characterized at the molecular level, the biochemical properties of the class II polymerases have not been studied in detail. Previously we and other groups purified the polymerases, however, the activities of the purified enzymes were several magnitude lower than the granule-bound enzymes. It is problematic to study the intrinsic properties of these enzymes with such low activities, although they are pure.

Utilization of solvent tolerant bacteria as biocatalysts has been suggested to enable or improve bioprocesses for the production of toxic compounds. Here, we studied the relevance of solvent (product) tolerance and inhibition, carbon metabolism, and the stability of biocatalytic activity in such a bioprocess. Styrene degrading Pseudomonas sp. strain VLB120 is shown to be solvent tolerant and was engineered to produce enantiopure (S)-styrene oxide from styrene. Whereas glucose as sole source for carbon and energy allowed efficient styrene epoxidation at rates up to 97 micromol/min/(g cell dry weight), citrate was found to repress epoxidation by the engineered Pseudomonas sp. strain VLB120DeltaC emphasizing that carbon source selection and control is critical. In comparison to recombinant Escherichia coli, the VLB120DeltaC-strain tolerated higher toxic product levels but showed less stable activities during fed-batch cultivation in a two-liquid phase system. Epoxidation activities of the VLB120DeltaC-strain decreased at product concentrations above 130 mM in the organic phase. During continuous two-liquid phase cultivations at organic-phase product concentrations of up to 85 mM, the VLB120DeltaC-strain showed stable activities and, as compared to recombinant E. coli, a more efficient glucose metabolism resulting in a 22% higher volumetric productivity. Kinetic analyses indicated that activities were limited by the styrene concentration and not by other factors such as NADH availability or catabolite repression. In conclusion, the stability of activity of the solvent tolerant VLB120DeltaC-strain can be considered critical at elevated toxic product levels, whereas the efficient carbon and energy metabolism of this Pseudomonas strain augurs well for productive continuous processing.

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Several cytochrome P450 alkane hydroxylases of the CYP153 family were recently identified and functionally expressed in Pseudomonas putida GPo12 [van Beilen JB, Funhoff EG, van Loon A, Just A, Kaysser L, Bouza M, et al. Cytochrome P450 alkane hydroxylases of the CYP153 family are common in alkane-degrading eubacteria lacking integral membrane alkane hydroxylases. Appl Environ Microbiol 2006;72:59–65]. Eight recombinants containing divergent CYP153's were cultivated on a 1.5–1.8L scale with octane or decane/dodecane as sole carbon source. Growth rates between 0.06 and 0.23h−1 were obtained and analysis of cell free extracts showed that the CYP153's were expressed to a maximum of 11% of total protein. The hydroxylation activities towards various substrates translate to maximal CYP153 turnover numbers between <0.1 and 58min−1. Aliphatic alkanes were exclusively hydroxylated on terminal carbon atoms. Epoxidation experiments with styrene, octene and cyclohexene showed turnover numbers that were slightly lower than the hydroxylation activities, with the exception of CYP153A11 and CYP153A14. The results provide insight in structural features that determine the substrate specificity of these enzymes.

ABSTRACT The first and key step in alkane metabolism is the terminal hydroxylation of alkanes to 1-alkanols, a reaction catalyzed by a family of integral-membrane diiron enzymes related to Pseudomonas putida GPo1 AlkB, by a diverse group of methane, propane, and butane monooxygenases and by some membrane-bound cytochrome P450s. Recently, a family of cytoplasmic P450 enzymes was identified in prokaryotes that allow their host to grow on aliphatic alkanes. One member of this family, CYP153A6 from Mycobacterium sp. HXN-1500, hydroxylates medium-chain-length alkanes (C 6 to C 11 ) to 1-alkanols with a maximal turnover number of 70 min −1 and has a regiospecificity of ≥95% for the terminal carbon atom position. Spectroscopic binding studies showed that C 6 -to-C 11 aliphatic alkanes bind in the active site with K d values varying from ∼20 nM to 3.7 μM. Longer alkanes bind more strongly than shorter alkanes, while the introduction of sterically hindering groups reduces the affinity. This suggests that the substrate-binding pocket is shaped such that linear alkanes are preferred. Electron paramagnetic resonance spectroscopy in the presence of the substrate showed the formation of an enzyme-substrate complex, which confirmed the binding of substrates observed in optical titrations. To rationalize the experimental observations on a molecular scale, homology modeling of CYP153A6 and docking of substrates were used to provide the first insight into structural features required for terminal alkane hydroxylation.

Several strains that grow on medium-chain-length alkanes and catalyze interesting hydroxylation and epoxidation reactions do not possess integral membrane nonheme iron alkane hydroxylases. Using PCR, we show that most of these strains possess enzymes related to CYP153A1 and CYP153A6, cytochrome P450 enzymes that were characterized as alkane hydroxylases. A vector for the polycistronic coexpression of individual CYP153 genes with a ferredoxin gene and a ferredoxin reductase gene was constructed. Seven of the 11 CYP153 genes tested allowed Pseudomonas putida GPo12 recombinants to grow well on alkanes, providing evidence that the newly cloned P450s are indeed alkane hydroxylases.

To determine whether microbial chemosensors can be used to find new or better biocatalysts, we constructed Escherichia coli hosts that recognize the product of a biocatalytic conversion through the transcriptional activator NahR and respond by expression of a lacZ or tetA reporter gene. Equipped with a benzaldehyde dehydrogenase (XylC from Pseudomonas putida), the lacZ-based host responded to the oxidation of benzaldehyde and 2-hydroxybenzaldehyde to the corresponding benzoic acids by forming blue colonies, whereas XylC- cells did not. Similarly, the tetA-based host was able to grow under selective conditions only when equipped with XylC, enabling selection of biocatalytically active cells in inactive populations at frequencies as low as 10(-6).

Functionalized medium-chain-length polyhydroxyalkanoates (mclPHAs) have gained much interest in research on biopolymers because of their ease of chemical modification. Tailored olefinic mclPHA production from mixtures of octanoic acid and 10-undecenoic acid was investigated in batch and dual (C,N) nutrient limited chemostat cultures of Pseudomonas putida GPo1 (ATCC 29347). In a batch culture, where P. putida GPo1 was grown on a mixture of octanoic acid (58 mol%) and 10-undecenoic acid (42 mol%), it was found that the fraction of aliphatic monomers was slightly lower in mclPHA produced during exponential growth than during late stationary phase. Thus, the total monomeric composition changed over time indicating different kinetics for the two carbon substrates. Chemostat experiments showed that the dual (C,N) nutrient limited growth regime (DNLGR) for 10-undecenoic acid coincided with the one for octanoic acid. Five different chemostats on equimolar mixtures of octanoic acid and 10-undecenoic acid within the DNLGR revealed that the monomeric composition of mclPHA was not a function of the carbon to nitrogen (C 0 /N 0 ) ratio in the feed medium but rather of the dilution rate. The fraction of aliphatic monomers in the accumulated mclPHA was slightly lower at high dilution rates and increased towards low dilution rates, again indicating different kinetics for the two carbon substrates in P. putida GPo1. © 2005 Wiley Periodicals, Inc.

The soluble bacterial epoxide hydrolase (EH) from Sphingomonas sp. HXN-200 catalyzed the enantioselective hydrolysis of racemic styrene oxide to give (S)-styrene oxide with an enantiomeric ratio (E) of 21–23 in aqueous buffer, better than any reported native EHs. The ring opening of the styrene oxide with this EH was only at the terminal position for the (S)-enantiomer and at the terminal and benzylic position in an 87:13 ratio for the (R)-enantiomer. Enzymatic hydrolysis of the styrene oxide in a two-liquid phase system significantly reduced autohydrolysis, thus improving the E to 26–29. Hydrolysis of 160mM styrene oxide with cell-free extract (CFE) of Sphingomonas sp. HXN-200 (10mg protein/mL) in aqueous buffer and n-hexane (1:1) for 30.7h afforded 39.2% (62.7mM) of (S)-styrene oxide in >99.9% ee. The lyophilized CFE was proven to be stable, while the rehydrated lyophilized CFE powder was successfully used for the hydrolysis of 320mM styrene oxide in the two-liquid phase system, yielding 40.2% (128.6mM) of (S)-styrene oxide in >99.9% ee after 13.8h. No inhibitory effect of the diol product on the hydrolysis was observed when the diol concentration was lower than 476mM, suggesting a straightforward process for the hydrolysis of up to 1M styrene oxide.

A process model for whole-cell biocatalysis in a two-liquid-phase system including cell growth and bioconversion kinetics was developed. The reaction considered is the kinetically controlled multistep oxidation of pseudocumene to 3,4-dimethylbenzaldehyde catalyzed by recombinant Escherichia coli expressing the Pseudomonas putida genes encoding xylene monooxygenase (XMO). XMO catalyzes the successive oxygenation of one methyl group of xylenes to corresponding alcohols, aldehydes, and acids. The biocatalytic process includes cells growing in fed-batch mode and a two-liquid-phase system consisting of bis( 2-ethylhexyl) phthalate as organic carrier solvent and an aqueous minimal medium in a phase ratio of 1: 1. The process model comprises a description of the bioconversion kinetics, mass transfer kinetics, cell growth, and mass balances for both the aqueous and the organic phase. Bioconversion kinetics and consistent process simulation indicated the occurrence of direct substrate uptake from the organic phase and provided evidence for a pH-influenced competition for NADH between XMO and the respiratory chain with its consequential impact on bioconversion and cell growth. For the simulation of such differential NADH limitation, a pH-dependent feedback inhibition of the NADH consuming bioconversions was introduced as a modeling tool, which allowed good simulations of biotransformation experiments performed at varying pH, scale, and initial substrate concentration. Moreover, modeling indicated a product inhibition in the second oxidation step, which could be confirmed experimentally. A sensitivity analysis for the aqueous-organic mass transfer coefficient showed that this transfer is not critical for the process performance and emphasized the efficient substrate-cell transfer in the investigated two-liquid-phase process. Based on a process model, this study provides an in-depth analysis of a biooxidation process based on growing cells with indications for biological energy shortage as a limiting factor.

Several nitrilases were screened for the hydrolysis of the nitrile group of cis-1,2-dihydroxy-3-cyanocyclohexa-3,5-diene and trans-3-[(5S,6R)-5,6-dihydroxycyclohexa-1,3-dienyl]-acrylonitrile to the corresponding acids. Nitrilase from Rhodococcus sp. was able to convert both compounds with the activity of 0.3mU/mg protein and 0.05mU/mg protein, respectively. Nitrilase AtNIT1 from Arabidopsis thaliana converted only the latter but with a higher initial specific activity of 1.7mU/mg protein. Biotransformation of trans-3-[(5S,6R)-5,6-dihydroxycyclohexa-1,3-dienyl]-acrylonitrile was performed with AtNIT1 in the form of isolated enzyme and immobilized enzyme, and with recombinant cells containing AtNIT1. Biotransformations with isolated AtNIT1 resulted in 116mg of product in 10.6h with a yield of 77%. Forty-three percent of the enzymatic activity could be recovered after the biotransformation. Immobilization of AtNIT1 saturated with 3-phenylpropionitrile resulted in 3.5% of the free enzyme activity. Biotransformations with Escherischia coli JM101 (pQE10-AtNIT1) in shake-flasks produced 243mg of product in 23h with a yield of 48%. Maximum and average specific activities of 0.5U/g cell dry weight and 0.17U/g cell dry weight were achieved, respectively.