Introduction

Organophosphorus compounds (OPs), one of the most frequently occurring components in pesticides and chemical warfare agents, are highly toxic and often hard to degrade. Examples of these OPs include the serine protease inhibitor diisopropylfluorophosphates (DFP) and G-type nerve agents such as soman (GD; O-pinacolyl methylphosphonofluoridate), sarin (GB; O-isopropyl methylphosphonofluoridate), and GF (O-cyclohexyl methylphosphonofluoridate). Exposure to OP compounds can irreversibly inhibit peripheral and central nervous system acetylcholinesterase (AChE). AChE is responsible for terminating the action of the neurotransmitter acetylcholine. Inhibition of this enzyme results in an accumulation of acetylcholine, which causes an over stimulation of muscarinic and nicotinic receptors, and even produces serious nerve agent poisoning including hypersecretion, convulsions, respiratory distress, coma, and death (Wetherell et al. 2006).

Currently, decontamination solutions such as DS2 and bleach are used to inactivate toxic OP compounds (Cheng et al. 1998). Despite their effective decontamination of OP compounds, both DS2 and bleach are very corrosive and result in hazardous waste production. While enzyme-based decontamination cocktails are being considered, the Defense Threat Reduction Agency (DTRA) recommends that enzymes to be used in these cocktails must have at least a 12-h pot-life reactivity over a range of conditions including different temperatures, pH, and in the presence of salts and other surfactants (DTRA 2008). Previously, organophosphorus acid anhydrolase (OPAA) isolated from Alteromonas sp. strain JD6.5, a halophilic organism, has been used for detoxification of DFP, sarin, soman, and tabun; however, OPAA demonstrates low hydrolysis of P–O and P–C bonds (DeFrank and Cheng 1991). Recently, the crystal structure of OPAA has been solved, and it was determined to be a prolidase (Vyas et al. 2010).

Prolidase is a ubiquitous dipeptidase that specifically cleaves dipeptides with proline at the C-terminus (NH2-X-/-Pro-COOH). This enzyme has been isolated and characterized from a variety of sources, such as from mammalian tissues (Browne and O’Cuinn 1983; Endo et al. 1987; Fukasawa et al. 2001; Myara et al. 1994; Sjostrom et al. 1973) as well as from bacterial and archaeal sources (Booth et al. 1990; Fernandez-Espla et al. 1997; Fujii et al. 1996; Ghosh et al. 1998; Jalving et al. 2002; Morel et al. 1999; Suga et al. 1995). The majority of the characterized prolidases contain a common “pita-bread” fold with a dinuclear metal center, which is generated by five conserved amino acid residues (Lowther and Matthews 2002). The OPAA crystal structure shares the same “pita-bread” fold with the characteristic catalytic dinuclear metal site. These findings indicate that prolidases can and are currently being used to decontaminate and detoxify OP exposed surfaces.

Among all prolidases that have been characterized so far, the ones that have been isolated from mesophilic sources are only maximally active at temperatures up to 55°C. However, prolidases that have been isolated from the hyperthermophilic archaea Pyrococcus furiosus and Pyrococcus horikoshii have maximum activity at 100°C. In addition, both recombinant Pyrococcus prolidases produced in Escherichia coli possess long-term thermostability. When incubated at 100°C, P. furiosus and P. horikoshii prolidases show no activity loss after 12 and 8 h, respectively (Ghosh et al. 1998; Theriot et al. 2009). P. horikoshii prolidases have a 50% activity loss after 21 h at 90°C (Theriot et al. 2009). The ability to maintain reactivity at high temperatures over long periods of time (pot-life activity) makes Pyrococcus prolidases ideal candidates for OP decontamination, where harsh conditions, such as high temperatures, organic solvents, and denaturants, are often required (Adams et al. 1995).

Despite the advantage P. furiosus prolidase exhibits under high temperature conditions, the use of P. furiosus prolidase for OP nerve agent decontamination is restricted by the fact that this enzyme displays a narrow functional temperature range. Like many other enzymes isolated from hyperthermophiles, P. furiosus prolidase has only 50% activity at 80°C and displays little activity at temperatures below 50°C (Ghosh et al. 1998). Therefore, it was desirable to attempt to prepare and screen P. furiosus prolidase mutants that demonstrate increased activity against OP compounds at low temperature while maintaining thermostability.

For these reasons, we constructed a random-mutated P. furiosus prolidase gene library and screened it for production of mutants with increased activity at room temperature. P. furiosus mutant prolidases were purified and characterized to determine their substrate catalysis over a range of temperature as well as their thermoactivity and thermostability compared to the wild-type enzyme.

Materials and methods

Bacterial strains and media

E. coli K-12 derivative NK5525 (proA::Tn10) was used to construct the selective strain JD1(λDE3) for screening of low-temperature active P. furiosus prolidase mutants. E. coli strains used in this study were cultured either in Luria–Bertani (LB) broth or M9 minimal medium supplemented with 0.2% glucose, 1 mM MgSO4, 0.05% thiamin, 20 μM IPTG, and 50 μM Leu-Pro. Ampicillin (100 μg/ml), kanamycin (50 μg/ml), chloramphenicol (34 μg/ml), and tetracycline (6 μg/ml) were added as required.

Construction of the E. coli selection strain JD1 (λDE3)

Selection strain JD1 (λDE3) was constructed as follows: (1) integration of λDE3 prophage into NK5525 chromosome by using a λDE3 lysogenization Kit (Novagen) according to the supplier’s protocol; (2) permanent disruption of proA in NK5525(λDE3) by removal of the chromosomal proA:Tn10 transposon using positive selection on fusaric acid media as described by Maloy and Nunn (1981); and (3) disruption of pepP and pepQ in NK5525(λDE3) by introducing chloramphenicol resistance (Cmr) and kanamycin resistance (Kmr) cassettes within each gene, respectively, using the λ-Red system (Datsenko and Wanner 2000). The Cmr cassette was amplified from the pKD3 plasmid using primer Ec PepP F and primer Ec PepP R (Table 1). The 5′ terminus of primer Ec PepP F and Ec PepP R had 50 and 52 nucleotides identical to sequences on the 5′-end and 3′-end of pepP, respectively; the Kmr cassette was amplified from the pKD4 plasmid using primer Ec PepQ F and primer Ec PepQ R (Table 1). The 5′ terminus of primer Ec PepQ F had 51 nucleotides identical to sequence upstream of pepQ, and the 5′ terminus of primer Ec PepQ R had 50 nucleotides identical to downstream sequence of pepQ. PCR-amplified products were purified using a commercial purification kit (Qiagen Germantown, MD, USA) and were integrated into the E. coli NK5525(λDE3) strain chromosome using the method developed by Datsenko and Wanner. The pepP and pepQ disruptions in NK5525(λDE3) were confirmed by PCR using primers PepP-Up and PepP-Dn and PepQ-Up and PepQ-Dn, respectively (Table 1).

Table 1 PCR and sequencing primers used in this study
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Construction of a pool of pET-prol plasmids carrying randomly mutated P. furiosus prolidase genes

To avoid biased results generated from a single mutagenesis method, random mutations were introduced into the gene encoding P. furiosus prolidase by three independent mutagenesis methods: error-prone PCR mutagenesis, hydroxylamine mutagenesis, and passage through mutation-prone E. coli XL1-red cells.

Error-prone PCR mutagenesis was done using the Genemorph II Random mutatgenesis kit. Mutazyme II DNA polymerase (Stratagene, La Jolla, CA, USA) was used to amplify the P. furiosus prolidase gene with the pET-prol expression plasmid serving as template (Ghosh et al. 1998). PCR amplification was carried out for 30 cycles (60 s at 95°C, 60 s at 55°C, 120 s at 72°C), with a 10-min final extension at 72°C. Reactions contained Mutazyme II reaction buffer, 125 ng/µl of each primer, 40 mM dNTP mix, and 2.5 U of Mutazyme II DNA polymerase. Initial DNA template amounts used were 50, 250, and 750 ng in order to select for high, medium, and low mutation rates, respectively. The Genemorph II EZClone (Stratagene) reaction was used to clone mutated prolidase genes into expression vector pET-21b according to the supplier’s protocol.

Hydroxylamine mutagenesis was conducted based on a previously described method (Grunden et al. 1996). P. furiosus prolidase gene (7.5 µg) was subjected to hydroxylamine mutagenesis. Hydroxylamine was removed using the PCR purification kit (Qiagen). Mutated prolidase gene fragments were digested with BamHI and NotI and were religated into pET-21b.

For XL1-red-based mutagenesis, mutation was directed against the intact pET-prol plasmid by transforming a pool of pET-prol plamsids into XL1-red cells seven times (Stratagene) according to the supplier’s protocol. The mutagenized prolidase genes were then isolated from the passaged pET-prol plasmids using BamHI and NotI restriction followed by religation into pET-21b vector.

Generation of the R19G/G39E/K71E/S229T mutant pET-prol plasmid

Production of the R19G/G39E/K71E/S229T pET-prol plasmid was carried out using the Site-Directed Mutagenesis kit (Stratagene). Two complementary oligonucleotide primers (Prol G39E F and Prol G39E R, Table 1) containing a mutation from glycine to glutamate at amino acid position 39 of R19G/K71E/S229T pET-prol plasmid were designed. These primers were used in a PCR reaction to amplify G39E pET-prol plasmid templates for 16 cycles (30 s at 95°C, 60 s at 55°C, and 7 min at 68°C). The PCR products were digested with DpnI prior to transformation into E. coli to remove un-mutated template DNA.

Screening for increased P. furiosus prolidase activity at low temperature (30°C)

pET-prol plasmids from the mutant P. furiosus library were transformed into the selection strain, JD1(λDE3), and were plated on M9 selective agar plates. Colonies that grew after being incubated for 3–7 days at room temperature were isolated and grown in 10 ml of LB medium at 37°C with shaking (200 rpm) until an optical density of 0.6–0.8 was reached. IPTG (1 mM) was then added to the cultures. Induced cultures were shaken at 37°C for 3 h before cell harvest. Cell pellets were lysed using 300 μl of B-PER reagent (Thermo Scientific, Rockford, IL, USA), and the resulting cell extracts were used for enzyme activity assays conducted at 30°C and 100°C. Mutant colonies that exhibited at least 2–3-fold higher activities compared to wild-type P. furiosus prolidase-expressing cells were selected and their plasmids were isolated. Prolidase genes from selected clones were sequenced using T7 promoter, prol-3, prol-4, and prol-5 and T7 terminator primers (Table 1) (MWG Biotech, Highpoint, NC, USA).

Purification of recombinant P. furiosus prolidase mutants

Production of P. furiosus prolidase and its variants G39E Pfprol, R19G/K71E/S229T Pfprol, and R19G/G39E/K71E/S229T Pfprol were carried out in E. coli BL21 (λDE3) that had been transformed with the appropriate pET-prol plasmid and pRIL vector. The transformants were grown in 1-L cultures in LB media and/or autoinduction media (Studier 2005) by incubation of the cultures at 37°C with shaking (200 rpm) until an optical density of 0.6–0.8 was reached. Expression of mutant prolidases was initiated when IPTG (1 mM) was added to the cell culture. Induced cultures were incubated at 37°C for 3 h prior to cell harvest. Autoinduction cultures were incubated overnight with shaking.

To purify G39E-, R19G/K71E/S229-, and R19G/G39E/K71E/S229T-prolidase, cell pellets were suspended in 50 mM Tris–HCl, pH 8.0, containing 1 mM benzamidine and 1 mM DTT (each 1 g wet wt of cell paste was suspended in 3 ml Tris–HCl buffer). Cell suspensions were passed through a French pressure cell (20,000 lb/in.2) twice. Lysed cell suspensions were centrifuged at 38,720 × g for 30 min to remove any cell debris, and supernatants were heat-treated at 80°C for 30 min anaerobically. Denatured protein was removed by centrifugation at 38,720 × g for 30 min. (NH4)2SO4 was slowly added to each heat-treated mutant prolidase extract to a final concentration of 1.5 M, and extracts were kept on ice until applied to a 20-ml phenyl-sepharose column. Fractions containing the prolidase mutants were further purified by passage through a Q column. In the case of purification of the G39E-prolidase mutant, an additional purification step through a gel-filtration column was also required. Buffers used for the phenyl-sepharose and Q column chromatography are previously described in Theriot et al. (2009). For the gel-filtration column, the equilibration buffer was 50 mM Tris–HCl, 400 mM NaCl, pH 8.0. All fractions were visualized on 12.5% SDS–polyacrylamide gels and were assayed for prolidase activity.

Enzyme activity assay

The enzyme activity assay used was based on a previously described method (Du et al. 2005; Theriot et al. 2009) with slight modification indicated below. Assay mixtures (500 µl) contained 50 mM MOPS buffer (3-[N-morpholino]propanesulfonic acid), 200 mM NaCl pH 7.0, 4 mM Xaa-Pro (substrate), 5% (vol/vol) glycerol, 100 µg/ml BSA protein, and 1.2 mM CoCl2. Assays were done in at least triplicate, and specific activities were calculated using the extinction coefficient of 4,570 M−1 cm−1 for the ninhydrin–proline complex (Theriot et al. 2009).

For assays conducted over a pH range, the reactions contained 200 mM NaCl and 50 mM of the following buffers: pH 4.0–5.0, sodium acetate; pH 6.0–8.0, MOPS; pH 9.0, CHES; pH 10.0, CAPS. When determining substrate specificity of the prolidases, the following dipeptides were used at a final concentration of 4 mM: Met-Pro, Leu-Pro, Phe-Pro, Ala-Pro, Gly-Pro, Arg-Pro, and Pro-Ala. To evaluate the enzyme kinetic parameters, enzyme assays were conducted at 35°C, 70°C, and 100°C with increasing concentrations of Met-Pro and a final metal concentration of 1.2 mM CoCl2.

Thermostability and pot-life activity assays

To measure the thermostability of wild-type P. furiosus prolidase and the mutant prolidases, each enzyme (0.04 mg/ml in 50 mM MOPS 200 mM NaCl, pH 7.0) was incubated in an anaerobic sealed vial at 90°C. Samples, taken at select time points, were used for enzyme activity assays that were conducted at 100°C and contained 4 mM Met-Pro and 1.2 mM CoCl2. To measure the pot-life reactivity of wild-type P. furiosus prolidase and the mutant prolidases, each enzyme (0.04 mg/ml in 50 mM MOPS 200 mM NaCl, pH 7.0) was incubated in an anaerobic sealed vial at 70°C. Samples were taken at 0, 6, 12, 24, 28, 32, and 48 h time points to assess the pot-life activity in reactions containing 4 mM Met-Pro and 1.2 mM CoCl2 at 100°C.

Organophosphorus nerve agent enzymatic assays

DFP assay

The method used was previously described in DeFrank and Cheng (1991). The hydrolysis of DFP by prolidases was measured by monitoring fluoride release with a fluoride specific electrode. Assays were performed at 35°C and 50°C, with continuous stirring in 2.5 ml of buffer (50 mM MOPS, 200 mM NaCl, pH 7.0), 0.2 mM CoCl2, and 3 mM DFP. The enzyme and metal were incubated at the reaction temperature 5 min prior to the start of the reaction. The background of DFP hydrolysis was measured by running a reaction without enzyme present at 35°C and 50°C. The background hydrolysis of DFP was subtracted from enzymatic hydrolysis to determine specific activity of the enzyme.

p-Nitrophenyl soman assay (O-pinacolyl p-nitrophenyl methylphosphonate activity)

Prolidase hydrolysis of p-nitrophenyl soman was monitored by accumulation of p-nitrophenyl (Hill et al. 2001; Vyas et al. 2010). Two-milliliter reaction assays contained buffer (50 mM MOPS, 200 mM NaCl, pH 7.0), 0.2 mM CoCl2, and 3 mM p-nitrophenyl soman. The reactions were conducted at three different temperatures (35°C, 50°C, and 70°C). The enzyme and metal were incubated at reaction temperature 5 min prior to the start of the reaction. Absorbance of the product p-nitrophenolate was measured at 405 nm over a 5 min range. To calculate activity, the extinction coefficient for p-nitrophenolate of 10,101 M−1 cm−1 was used.

Results

Isolation of P. furiosus prolidase mutants with increased activity over a broader range of temperature

P. furiosus prolidase loses 50% of its activity at 80°C and has limited activity at temperatures below 50°C (Ghosh et al. 1998). Therefore, its gene sequence must be altered in order to obtain variants of P. furiosus prolidase that exhibit higher catalytic activity at lower temperatures (10°C to 70°C). To achieve this goal, the gene encoding P. furiosus prolidase was randomly mutagenized and subsequently cloned back into expression vector pET-21b to generate a pool of mutant pET-prol plasmids. Clones of the desired phenotype were positively selected by genetic complementation of an E. coli selective strain JD1(λDE3) that has deletions of proA, pepP, and pepQ genes (ΔproA, ΔpepP, and ΔpepQ). The proA gene encodes γ-glutamylphosphate reductase, the enzyme responsible for the third step in proline biosynthesis, conversion of l-γ-glutamyl phosphate to γ-glutamic semialdehyde, and pepP and pepQ are the only two genes in the E. coli genome that code for dipeptidases with specificity for proline-containing dipeptides. As a consequence of these deletions, JD1(λDE3) is incapable of growing on minimal media supplied with Leu-Pro as the only proline source.

JD1(λDE3) cells were transformed with plasmids carrying mutant P. furiosus prolidase genes. The transformed cells were plated on minimal media supplemented with Leu-Pro, and the plates were incubated at room temperature. Because wild-type P. furiosus prolidase could not support growth of the JD1(λDE3) cells at the temperatures that permit growth of E. coli, colonies that survived and grew on the selective plates would have to have been able to produce cold-adapted variants that had higher activity than the wild-type enzyme at these lower temperatures. Using this positive selection, approximately 500 colonies were isolated and screened. To avoid false results that could come from variation in enzyme production levels, the mutant prolidase expression plasmids were isolated from colonies on the original selection plates and were transformed into both JD1(λDE3) and BL21(λDE3). The resultant transformants were screened for prolidase activity, and those isolates that exhibited at least 2–3-fold higher activity at 30°C compared to cells expressing wild-type prolidase were retained for further evaluation. Results of this study led to the identification of two mutants with increased activity at low temperature, with one containing a single mutation at amino residue 39 (G39E) and the other containing a triple mutation at amino residues R19G, K71E, and S229T, a change from arginine to glycine at position 19, a change from lysine to glutamate at position 71, and serine to threonine at position 229.

To avoid biased results that may be generated from a single mutagenesis method and to construct a library of P. furiosus prolidase expression plasmid mutants with a good variety of mutation types, three mutagenesis methods were employed, which included error-prone PCR using Genemorph mutazyme polymerase, hydroxylamine mutagenesis, and passage of the prolidase expression plasmid through mutation-prone E. coli strain XL1-red. This strategy proved to be successful with the G39E-prolidase mutant arising from XL1-red cell mutagenesis and the R19G/K71E/S229T-prolidase mutant being generated using the Genemorph II random mutagenesis method.

Construction and purification of a third prolidase mutant: R19G/G39E/K71E/S229T-prolidase

To gain further insight into the effects of cold-adapted substitutions on the P. furiosus prolidase, another variant R19G/G39E/K71E/S229T-prolidase (a combination of all four mutations) was produced. Specifically, the G39E-, R19G/K71E/S229T-, and R19G/G39E/K71E/S229T-prolidases were over-expressed by large-scale expression in BL21(λDE3) cells and were purified through a multi-column chromatography strategy. Each protein was successfully purified and was shown to have a molecular weight of approximately 39.4 kDa. The purified prolidases were used for subsequent enzyme assays.

Locations of amino acid substitutions in the mutants

The three-dimensional model of P. furiosus prolidase had previously been solved and its structural characteristics well evaluated (Maher et al. 2004). This structure was used to analyze the position and possible interactions of each of the amino acid substitutions found in the G39E- and R19G/K71E/S229T- and R19G/G39E/K71E/S229T-prolidase mutants (Fig. 1a/b).

Fig. 1
figure 1

Mapping of the mutations in the monomer structure of P. furiosus prolidase and OPAA/prolidase from Alteromonas sp. strain JD6.5. Mutations made in the Pfprol are indicated by red circles and include R19G, G39E, K71E, and S229T. a Stereoview of the backbone trace of the domain structure. b Ribbon drawing of the domain structure in the same orientation as a. N-terminal domain is in blue, and the C-terminal domain is in yellow. The metal atoms are depicted as gray spheres (modified from Maher et al. 2004). c Ribbon drawing of the Alteromonas sp. strain JD6.5 OPAA/prolidase monomer (modified from Vyas et al. 2010)

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Effects of the amino acid substitutions on the catalytic activity of P. furiosus prolidase at different temperatures

To study whether the substitutions affect the activity of P. furiosus prolidases over a range of temperatures, the kinetic parameters of G39E-, R19G/K71E/S229T-, and R19G/G39E/K71E/S229T-prolidase were measured at 35°C, 70°C, and 100°C (Table 2). All mutants performed better at 35°C compared to wild-type Pfprol, as each mutant exhibited higher V max and k cat values than wild-type prolidase. Although these values were higher, so was the K m suggesting changes or increases in flexibility of the binding pocket. A similar trend was seen at the higher assay temperatures. At 70°C, the K m’s were observed to be 1.6-fold higher for R19G/K71E/S229T-prolidase than WT-Pfprol, and the K m for R19G/G39E/K71E/S229T-prolidase was 1.3-fold higher than WT-Pfprol. The V max and the k cat values for R19G/G39E/K71E/S229T-prolidase were both 3.2-fold higher than WT at 70°C. The k cat /K m value for R19G/G39E/K71E/S229T-prolidase showed the highest value at 2.4-fold higher than the wild-type prolidase. This trend continued at 100°C, where the K m, V max, k cat, and k cat /K m for the mutant prolidases were all higher than WT-Pfprol. At higher temperatures, as the number of mutations increase, so did the enzyme reaction rate. At 100°C, the k cat /K m were 1.2-, 1.8-, and 2.5-fold higher than WT for G39E-, R19G/K71E/S229T-, and R19G/G39E/K71E/S229T-prolidase, respectively. Mutated prolidases showed overall improved enzyme activity and reaction rates at all three temperatures when compared to WT-Pfprol.

Table 2 Kinetic parameters of wild-type and mutated prolidases from Pyrococcus furiosus
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When examining the relative activity of prolidases with the substrate Met-Pro (4 mM) (Fig. 2), there were differences observed between WT-Pfprol and the mutants at temperatures ranging from 10°C to 100°C. The most dramatic differences were seen in the improved activity of G39E-, R19G/K71E/S229T-, and R19G/G39E/K71E/S229T-prolidase mutants at 10°C with 2.3-, 3.5-, and 5.1-fold increases in relative activity, respectively, compared to wild-type activity. The improved activity of R19G/G39E/K71E/S229T-prolidase was seen at all temperatures, but was especially evident at 50°C, in which it showed a 2.9-fold increase in activity relative to wild-type prolidase. It is intriguing to find that the increased activities of the G39E mutation at the low-temperature range came at the expense of decreased activity at the high temperature range. Specifically, G39E-prolidase had lower activity at 70°C, exhibiting 83% of the activity of wild type; however, it did not seem to have compromised activity when assayed at 100°C, since it was observed to have 103% of the activity detected for the wild-type prolidase. This dip in activity at the higher temperatures was not seen with the R19G/K71E/S229T- and R19G/G39E/K71E/S229T-prolidase mutants. The R19G, K71E and S229T mutations appeared to significantly increase the activity and improve the rate of catalysis of the P. furiosus prolidase.

Fig. 2
figure 2

Relative activity of WT-Pfprol and the prolidase mutants with Met-Pro (4 mM) and CoCl2 (1.2 mM) at temperatures ranging from 10°C to 100°C. One hundred percent relative activity corresponds to WT-Pfprol specific activities of 5.5 U/mg at 10°C, 25 U/mg at 20°C, 61 U/mg at 35°C, 138 U/mg at 50°C, 806 U/mg at 70°C, and 2,154 U/mg at 100°C

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Effect of the amino acid substitutions on the pH optimum of P. furiosus prolidase

Effects of the substitutions on the pH optima of the wild-type and mutant enzymes were analyzed by measuring activities of G39E-, R19G/K71E/S229T-, and R19G/G39E/K71E/S229T-prolidase mutants at 100°C from pH 4 to 10 with the wild-type enzyme serving as the reference. As shown in Fig. 3, the catalytic activities of G39E- and R19G/G39E/K71E/S229T-prolidase have similar responses to changes in pH, as both showed optimal activities at pH 6.0 and pH 7.0, although the activity was 60% and 89% of wild-type activity, respectively. These proteins both include the G39E mutation, which strongly suggests that Gly39 plays an important role in maintaining the integrity of the active site, and the substitution of this residue with glutamate greatly reduces enzyme activity at optimal pH and high temperature.

Fig. 3
figure 3

Specific activity of WT-Pfprol and prolidase mutants over a pH range of 4.0–10.0. Prolidase assays were done at 100°C and contained Met-Pro (4 mM), CoCl2 (1.2 mM), and a final concentration of 200 mM NaCl and 50 mM of the following buffers: pH 4.0–5.0, sodium acetate; pH 6.0–8.0, MOPS; pH 9.0, CHES; pH 10.0, CAPS

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In contrast, R19G/K71E/S229T-prolidase showed increased activity over the pH range of 5–7. At pH 5.0, the mutant activity was 1.6-fold higher than wild-type activity, and at pH 7.0, it was 1.2-fold higher than wild type. In addition, the activity was somewhat less affected than the other mutants at pH 6.0 and pH 8.0, showing similar activities to wild type. It was noticed that the optimal pH for the activity of P. furiosus prolidase presented in our study is pH 6.0, which is different from the previous report of pH 7.0 (Ghosh et al. 1998). The reason for the pH optimum shifting is not known; however, it might be the result of the use of different protein expression and purification methods.

Effect of the amino acid substitutions on the thermostability and pot-life activity of P. furiosus prolidase

To study whether the substitutions affected enzyme thermostability, the mutated prolidases were incubated at 90°C under anaerobic conditions, and their catalytic activities were measured at specific time points. For these activity assays, Met-Pro (4 mM) was used as the substrate (see “Materials and methods”). Although the R19G/K71E/S229T- and R19G/G39E/K71E/S229T-prolidase showed higher activity over a broad range of temperatures, the thermostability of these enzymes was less compared to wild type. R19G/K71E/S229T- and R19G/G39E/K71E/S229T-prolidase lost 50% activity after 4 and 3 h at 90°C, respectively, whereas G39E-prolidase did not show this loss of activity until 14 h, and WT-Pfprol did not lose 50% activity until 21 h had elapsed. The increased number of substitutions resulted in decreases in long-term stability of prolidases at the physiologically relevant temperature of 90°C.

The pot-life activity was assessed over a 3-day period with constant incubation at 70°C (Fig. 4). After 12 h, all the prolidases were capable of degrading Met-Pro (4 mM) with specific activities of 1,563, 1,768, 843, and 1,366 for WT-, G39E-, R19G/K71E/S229T-, and R19G/G39E/K71E/S229T-prolidase, respectively. After 48 h, the prolidases were still functional and had activities of 1,083, 599, 722, and 496 U/mg for WT-, G39E-, R19G/K71E/S229T-, and R19G/G39E/K71E/S229T-prolidase, respectively

Fig. 4
figure 4

Pot-life activity of WT-Pfprol and prolidase mutants at 70°C. Prolidase assays were performed at 100°C and contained 1.2 mM CoCl2 and 4 mM of Met-Pro. P. furiosus prolidases were incubated anaerobically at 70°C over a 48-h period. Enzyme samples were taken after 12, 24, and 48 h to assess reactivity

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Effect of the amino acid substitutions on the substrate specificity of P. furiosus prolidase

Table 3 shows the relative activity of mutants compared to WT-Pfprol with other prolidase specific dipeptides. For the substrate Met-Pro, there was little difference between the activity observed for the wild type when compared to G39E-prolidase, but an increase in activity occurred with R19G/K71E/S229T- and R19G/G39E/K71E/S229T-prolidase mutants, showing 137% (2,886 U/mg) and 143% (3,080 U/mg) activity of wild type with Met-Pro, respectively. There was a more significant increase seen for R19G/K71E/S229T-prolidase when assayed with Leu-Pro, as it had 169% (2,674 U/mg) of the wild-type prolidase activity with Leu-Pro. This surpasses the activity of WT with Met-Pro, which has a specific activity of 2,154 U/mg. This higher activity for the R19G/K71E/S229T-prolidase mutant could be due to the addition of Leu-Pro in the positive selection method used to isolate the low-temperature active mutants, in effect selecting an enzyme that prefers and is more active with Leu-Pro. When the G39E substitution was made in the prolidase, the enzyme activity decreased when Leu-Pro was used as the substrate, suggesting that this particular mutation could be hindering substrate specificity with Leu-Pro. The dipeptide Phe-Pro showed the highest activity with R19G/G39E/K71E/S229T-prolidase at 122% activity of wild type, whereas G39E- prolidase had the lowest detected activity at 60% of wild type. The mutants all showed decreased activity with Ala-Pro and Gly-Pro. The incorporation of mutation G39E seemed to substantially reduce activity with both substrates, showing 35% and 38% activity of wild type for Ala-Pro and 37% and 10% for Gly-Pro for G39E- and R19G/G39E/K71E/S229T-prolidase, respectively. Activity for R19G/K71E/S229T-prolidase with Gly-Pro was 47% of wild type, but was fairly unaffected when Ala-Pro was used as the substrate, maintaining 95% of wild-type activity. Relative activities with Arg-Pro all went up for the mutants relative to the activity of wild type, which was reported as 164 U/mg. As for Pro-Ala, a substrate that is not usually hydrolyzed by prolidases, even though mutant prolidase activities increased relative to WT, it is important to note that the starting activity of WT was very low to begin with at 24 U/mg.

Table 3 Substrate specificity of recombinant wild-type and mutant P. furiosus prolidase with different proline dipeptides
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Effect of the substitutions on substrate specificity with OP nerve agents DFP and soman analog, p-nitrophenyl soman

Increases in activity at lower temperatures with Xaa-Pro dipeptides, which is thought to be the physiologically relevant substrate of prolidases, were also observed for the P. furiosus prolidase mutants when OP nerve agents, DFP and p-nitrophenyl soman, served as the substrate. In Fig. 5, the relative activity of the prolidase mutants and WT-Pfprol with DFP as the substrate can be seen. The G39E substituted prolidase exhibited increases in relative activities that were 2- and 2.2-fold higher than wild-type activity with DFP at temperatures 35°C and 50°C. R19G/G39E/K71E/S229T-prolidase showed the highest activity at 50°C with 7.5-fold higher activity than wild type. The addition of the G39E mutation to the R19G/K71E/S229T prolidase substitutions had in this case increased the activity with DFP as the substrate, whereas R19G/K71E/S229T-prolidase had decreased activity with DFP (71% activity compared to wild type).

Fig. 5
figure 5

Relative activity with WT-Pfprol and prolidase mutants with OP nerve agent DFP. All prolidase assays contained 50 mM MOPS 200 mM NaCl pH 7.0, 0.2 mM CoCl2, and 3 mM DFP. One hundred percent relative activity corresponds to WT-Pfprol specific activity for DFP of 0.42 µmol product formed per minute per milligram at 35°C and 0.73 µmol product formed per minute per milligram at 50°C

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Activity with p-nitrophenyl soman is even more promising with all three mutant prolidases showing significant activity at 35°C, 50°C, and 70°C (Fig. 6). As the temperature increases, there was increased hydrolysis of p-nitrophenyl soman, which is characteristic of a hyperthermophilic enzyme. The highest activity can be seen with R19G/G39E/K71E/S229T-prolidase, with a 3.4-fold increase in activity over WT at 70°C. It is interesting to note that P. furiosus prolidase mutants all showed increased activity compared to WT-Pfprol with p-nitrophenyl soman at all temperatures that were evaluated.

Fig. 6
figure 6

Relative activity with WT-Pfprol and prolidase mutants with the OP nerve agent analog, p-nitrophenyl soman. All prolidase assays contained 50 mM MOPS 200 mM NaCl pH 7.0, 0.2 mM CoCl2, and 3 mM p-nitrophenyl soman. One hundred percent relative activity corresponds to WT-Pfprol specific activity of p-nitrophenyl soman of 0.23 µmol product formed per minute per milligram at 35°C, 0.3 µmol product formed per minute per milligram at 50°C, and 0.5 µmol product formed per minute per milligram at 70°C

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Table 4 shows a comparison of the specific activities of wild-type and mutant P. furiosus prolidases with Alteromonas sp. strain JD6.5 OPAA/prolidase, an enzyme presently being studied for its use in enzyme decontamination cocktails. R19G/G39E/K71E/S229T-prolidase showed the highest activity with substrates DFP and soman analog, but a 90% decrease with Gly-Pro compared to WT-Pfprol. When comparing these activities to OPAA/prolidase (Vyas et al. 2010), R19G/G39E/K71E/S229T-prolidase exhibited 1%, 267%, and 35% the total activity of OPAA/prolidase for substrates DFP, Gly-Pro, and p-nitrophenyl soman, respectively.

Table 4 Specific activity of OP nerve agents and Gly-Pro with Alteromonas sp. strain JD6. 5 OPAA/prolidase and Pyrococcus furiosus prolidases
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Discussion

Using a positive selection strategy (directed evolution), three cold-adapted P. furiosus prolidase variants were screened, purified, and characterized. Because the substitutions occurred at different locations in the protein structure, G39E- and R19G/K71E/S229T- and R19G/G39E/K71E/S229T-prolidase each exhibit different responses toward the changes in temperature, pH, substrate specificity, and thermostability.

It has been previously reported by Lebbink et al. (2000) and Suzuki et al. (2001) that increased activity at low temperature is accompanied by lower activity at high temperature in the screen for cold-adapted hyperthermophilic enzymes. This can also be referred to as the activity–stability trade off because it too is accompanied by a decrease in thermostability (Zecchinon et al. 2001). Our study supports this theory since the R19G/K71E/S229T- and R19G/G39E/K71E/S229T-prolidase mutants demonstrated not only an increased activity at lower temperatures but also a decrease in thermostability at 90°C, in which enzyme activity fell by half in the first 3–4 h of incubation at 90°C. However, thermoactivity of these two mutants at 100°C did increase, but at a cost of stability at high temperatures. Although the exact mechanism behind the observed changes in thermostability is still unclear at this stage, it has been suggested that protein thermostability is not maintained by a single mechanism. Instead, it is fostered by a network of numerous factors, including increased van der Waal interactions (Berezovsky et al. 1997), higher core hydrophobicity (Schumann et al. 1993), additional networks of hydrogen bonds (Jaenicke and Bohm 1998), enhanced secondary structure propensity (Querol et al. 1996), ionic interactions (Vetriani et al. 1998), increased packing density (Hurley et al. 1992), and decreased length of surface loops (Thompson and Eisenberg 1999). In Table 4, a comparison of the hydrolysis of OP nerve agents, DFP, p-nitrophenyl soman, and prolidase specific substrate, Gly-Pro, between the prolidases from Alteromonas sp. strain JD6.5 and P. furiosus was shown (Vyas et al. 2010). This is the first study demonstrating that P. furiosus prolidases are able to hydrolyze OP nerve agents, DFP and p-nitrophenyl soman, with the mutants exhibiting higher activity at lower temperature relative to WT-Pfprol. The wild-type and mutant P. furiosus prolidases all remain reactive at 12 h and even up to 48 h when incubated at 70°C, which is promising given the DTRA guidelines. The development of an enzyme-based cocktail for response decontamination of chemical warfare agents is being considered by the US Department of Defense and requires that enzyme catalysts retain reactivity in solutions over a range of temperatures and have a pot life of at least 12 h. Other desirable qualities include enzymes that are active and stable over broad ranges of pH and remain functional in the presence of salts and other surfactants. It would be beneficial to include OPAA/prolidase in a cocktail, along with other prolidases, such as the mutant P. furiosus prolidases that are stable and active over a broad temperature and pH range.

The ability of OPAA to hydrolyze OP nerve agents in addition to Xaa-Pro dipeptides has been observed for many years, while the reaction mechanism has taken longer to elucidate (Cheng et al. 1998, 1999). OPAA/prolidase has the same pita-bread fold in the C-terminal region as do prolidases and also contains a binuclear Mn(II) active site with metal ligand residues Asp-244, Asp-255, His-336, Glu-381, and Glu-420 with bound glycolate, a surrogate of glycine (Vyas et al. 2010). These residues are homologous in most pita-bread enzyme C-terminal catalytic domains, including enzymes methionine aminopeptidase and aminopeptidase P (AMPP) (Lowther and Matthews 2002). P. furiosus prolidase is almost identical to OPAA, although it contains a Co(II) dinuclear active site consisting of metal ligand residues Asp-209, Asp-220, His-284, Glu-313, and Glu-327, with a bridging water molecule at W176 (Maher et al. 2004). Detailed comparisons of AMPP and OPAA indicated that the substrate specificity is similar due to the hydrophobic proline binding pocket provided by residues His-350 and Arg-404 in AMPP that interact with the prolidyl ring of substrate P1′ Pro; these interactions and residues are conserved in OPAA/prolidase at His-332 and Arg-418 (Graham et al. 2006). The reaction mechanism of these two enzymes is similar, where in Pfprol, the bridging hydroxide nucleophile, attacks the carbonyl oxygen of the scissile peptide bond of the dipeptide substrate, and it also can attack the phosphorus center of OP nerve agents, like DFP, which explains the crossover in substrate specificity (Lowther and Matthews 2002; Vyas et al. 2010). However, there could be subtle differences introduced when the four subunits form a tetramer of AMPP, whereas only one subunit forms the monomer of OPAA/prolidase (Fig. 1c).

This study provides experimental evidence that supports the idea that through the use of directed evolution methods, thermophilic enzymes can be engineered to yield cold-adapted variants. Our efforts focused on the improvement of P. furiosus prolidase activity at low temperatures (10°C to 70°C) and resulted in identification of amino acid residues critical in supporting low-temperature activity of the enzyme.