Production of cis,cis-muconic acid by catechol 1,2-dioxygenase
In last few decades enzymes with potential for usage in chemical synthesis at the industrial scale have been sought. It is especially important for production of stereoisomers since enzymes exhibit regioselectivity and stereoselectivity (Ran et al. 2008). Several studies have demonstrated production of cis,cis-muconic acid by microorganisms from benzene, toluene, benzoic acid or catechol (Bang and Choi 1995; Bang et al. 1996; Frost and Draths 1996, 1997). For example, a mutant strain of Arthrobacter sp. produced 44 g/l of cis,cis-muconic acid in two days of culture (Mizuno and Yoshikawa 1990). For the further enhancement of the cis,cis-muconic acid productivity, it is necessary to obtain high activity catechol 1,2-dioxygenase, the key enzyme in the cis,cis-muconate biosynthetic pathway (Kim et al. 1998; Wu et al. 2006). An earlier study showed that catechol 1,2-dioxygenase from S. maltophilia KB2 was observed after growing the strain in the presence of benzoate (Wojcieszyńska et al. 2011). We considered that the formation of this compound is dependent on substrate concentration. Figure 1 shows that the rate of cis,cis-muconic acid synthesis averaged 10 μM/min. The molar conversion yield based on the amount of consumed catechol was the theoretical value of 100 % (mol/mol). Similar results was obtained by Kaneko et al. (2011) during production of cis,cis-muconic acid by recombinant E. coli cells that expressed a catA gene from Pseudomonas putida mt-2.
Sequence analysis of the catechol 1,2-dioxygenase gene
Genes encoding catechol dioxygenases can be located on plasmids or/and on the chromosome (Neidle et al. 1998; Sauret-Ignazi et al. 1996;Vaillancourt et al. 2006; Wojcieszyńska et al. 2011). Our research indicated that strain KB2 contains plasmid DNA (Wojcieszyńska et al. 2011) and we thus performed PCR with chromosomal and plasmid DNA as a template. To amplify the catechol 1,2-dioxygenase S. maltophilia KB2 gene we used primers 1,2D_zewF and 1,2D_zewR (Guzik et al. 2011). A PCR product was obtained only with chromosomal DNA as a template, indicating that the gene is located on the chromosomal DNA. Sequencing of the PCR product resulted in a 1243 nucleotide sequence (deposited in GenBank under accession number EU000397). A phylogenetic tree was created (Fig. 2), based upon the catechol 1,2-dioxygenase gene sequences found in GenBank and the new sequence obtained in this study. There was high homology found with other intradiol dioxygenase genes.
Structural properties of the catechol 1,2-dioxygenase
Knowledge of the catechol 1,2-dioxygenases 3-D structure can provide the important information into the molecular mechanisms of these enzymes. The deduced 314-residue amino acid sequence of S. maltophilia KB2 (deposited in the GenBank under accession number ABS86780.1) enzyme corresponds to a protein of molecular mass 34.5 kDa. Similar molecular weights for dioxygenase from Acinetobacter calcoaceticus and P. putida N6 were obtained by Neidle et al. (1998) and Guzik et al. (2011), respectively.
We predicted the 3-D structure of the catechol 1,2-dioxygenase from strain KB2 based on the deduced amino acid sequence by using the interactive mode of the 3D-JIGSAW protein comparative modeling server. Catechol 1,2-dioxygenase from strain KB2 (Fig. 3a) probably possesses an N-terminal domain with five α helices and a C-terminal domain consisting of β-sheets–structures typical for other intradiol dioxygenases as reported previously (Guzik et al. 2011; Ohlendorf et al. 1994; Vaillancourt et al. 1998). Similar molecular structure was also noted in another study of Pseudomonas arvilla C-1 catechol 1,2-dioxygenase, catechol 1,2-dioxygenase and 4-chlorocatechol 1,2-dioxygenase from Rhodococcus opacus 1CP (Earhart et al. 2005; Ferraroni et al. 2004; Matera et al. 2010). The α helices localized within N-terminal domain of the enzyme of strain C-1, like other known intradiol enzymes, were found to be involved in dimerization of enzyme subunits (Bugg 2003; Vaillancourt et al. 2006; Wojcieszyńska et al. 2011).
Intradiol dioxygenases coordinate ferric ion by two histidine, two tyrosine residues and one hydroxyl ion in a trigonalbipyramidal geometry (Bruijnincx et al. 2008; Bugg and Lin 2001; Earhart et al. 2005; Ferraroni et al. 2004; Matera et al. 2010; Melo et al. 2010). Within the active site of the R. opacus 1CP 4-chlorocatechol 1,2-dioxygenase, the coordination residues were identified at positions His-194, His-196, Tyr-134, and Tyr-169 (Ferraroni et al. 2004). The catechol 1,2-dioxygenase isolated from this same strain possess as iron ligands: Tyr-162, Tyr-196, His-220, and His-222 (Matera et al. 2010). Our work predicts His-226 Tyr-166, and Tyr-200 to be involved in ferric ions coordination (Figs. 3b, c, 4). However, comparison of the deduced amino acid sequence of the catechol 1,2-dioxygenase from S. maltophilia KB2 with other catechol 1,2-dioxygenases has shown that one of conserved active-site residues was altered in the strain KB2 sequence. We predict Gln-224 as a fourth ligand of iron ion (Fig. 4). Displacing one of the key iron bound ligands can cause changes in catalytic properties of enzyme and therefore we examined these in our study.
Kinetic properties of catechol 1,2-dioxygenase in S. maltophilia KB2 cell extracts
The pH-activity and temperature-activity curves showed that the maximum catechol 1,2-dioxygenase activity (3,062 U/mg protein) was at pH 8 and 40 °C, respectively (Fig. 5a, b). On the other hand, the examined enzyme was not very stable in this temperature (Fig. 5c). The half-life of the enzyme at 40 °C was 3 h (Fig. 5b). Interestingly, the enzyme lost 16.5 % of its enzymatic activity at 50 °C and the activity rapidly declined at 55 °C (Fig. 5b). A similar effect was observed by Wang et al. (2006) and Murakami et al. (1998) for catechol 1,2-dioxygenase from Pseudomonas aeruginosa and Arthrobacter species BA-5-17, respectively. The enzyme isolated from strain KB2 lost 100 % of its original enzymatic activity at pH 2.2 and about 83 % at pH 12.0 (Fig. 5a). The optimal pH of the catechol 1,2-dioxygenase is high compared with that of catechol 1,2-dioxygenase from Pseudomonas fluorescens,
P. aeruginosa and Rhodococcus sp. NCIM2891 (Nadaf and Ghosh 2011; Saxena and Thakur 2005; Wang et al. 2006).
In order to calculate values of K
m and V
max parameters, the activity of the S. maltophilia KB2 catechol 1,2-dioxygenase was measured at different substrate concentrations as detailed in Materials and Methods. The K
m and V
max values obtained were 12.18 μM and 1,218.8 U/mg of protein, respectively (Fig. 5d). This V
max value is notably higher (approximately 20–100-fold) than the activity of other catechol 1,2-dioxygenases. Catechol 1,2-dioxygenase form Acinetobacter radioresistens showed 25.8 U/mg of protein (Briganti et al. 2000). Suvorova et al. (2006) and Solyanikova et al. (2009) characterized catechol 1,2-dioxygenase from R. opacus 1CP and R. opacus 6a with activities of 9.6 U/mg of protein and 55.5 U/mg of protein, respectively. Of note, the K
m value was 2-fold higher than those obtained by Wang et al. (2006) and Nadaf and Ghosh (2011). This result may therefore indicate lower affinity of enzyme to the substrate.
During our studies on kinetic properties of the catechol 1,2-dioxygenase, substrate inhibition at >80 μM was observed (Fig. 5d). In line with our results, Sauret-Ignazi et al. (1996) observed inhibition activity of an Alicaligenes eutrophus CH34 1,2-dioxygenase which catalyses tetrachlorocatechol degradation.
Influence of various substrates on catechol 1,2-dioxygenase activity in S. maltophilia KB2 cell extracts
Differences in substrate specificity is one of the interesting characteristics noted among the isofunctional dioxygenases from various sources. The relative activities of the catechol 1,2-dioxygenase from strain KB2 towards various substrates are given in Table 1. It was found that the enzyme showed activity against catechol, 3-methylcatechol, and 4-methylcatechol. No activity was observed for 3-chloro- and 4-chlorocatechol, 3,5-dichloro- and 4,5-dichlorocatechol and hydroquinone. It could be interpreted that a haloatom might prevent the dioxygenase from attacking the ring. Similar results were obtained by Briganti et al. (2000), Matsumura et al. (2004) and Murakami et al. (1998) for intradiol dioxygenases isolated from A. radioresistens, Rhodococcus sp. AN-22 and Arthrobacter species BA-5-17, respectively. Giedraityte and Kalediene (2009) reported only 27 and 6 % of the relative activity to catechol (7.42 U/mg of protein) of a catechol 1,2-dioxygenase from Geobacillus sp. towards 3-methylcatechol and 4-methylcatechol, respectively. Remarkably broader substrate specificity was described by Wang et al. (2006) and Guo et al. (2009) during characterization of catechol 1,2-dioxygenases from P. aeruginosa and Sphingomonas xenophaga QYY, respectively. The catechol 1,2-dioxygenase from R. opacus 1CP showed high activity against to catechol and methylcatechols. Moreover, this enzyme catalyzed cleavage of chlorocatechols, pyrogallol, hydroxyquinol, 2,3- and 3,4-dihydroxybenzoic acid ring (Matera et al. 2010).
Table 1 Substrate specificity of catechol 1,2-dioxygenase from S. maltophilia KB2
Enzyme activity in S. maltophilia KB2 cell extracts in the presence of inhibitors
Phenols substituted in the ortho position, which structurally mimic catechols, are known as competitive inhibitors of catechol 1,2-dioxygenases because they coordinate to the iron (III) ion in the enzyme active site (Sauret-Ignazi et al. 1996; Vaillancourt et al. 1998). Most of the phenols studied affected enzyme activity at all tested concentrations (Table 2). Sauret-Ignazi et al. (1996) observed greater sensitivity of catechol 1,2-dioxygenase in the presence of para substituted phenols. However the catechol 1,2-dioxygenase from strain KB2 strain did not reveal dependence of activity changes on position and kind of substituents. A similar effect was observed by Kolomytseva et al. (2010) during analysis of the influence of monochloro- and monomethylphenols on activity of chlorocatechol 1,2-dioxygenases from Rhodococcus opacus 1CP.
Table 2 Effect of phenols and chelators on the activity of catechol 1,2-dioxygenase from S. maltophilia KB2
The sensitivity of the catechol 1,2-dioxygenase from strain KB to both ferrous and ferric iron chelators (Table 2) may reflect the fact that the iron of the enzyme active site is more weakly bound than in the enzyme from Arthrobacter species BA-5-17 (Murakami et al. 1998), Trichosporon cutaneum (Varga and Neujahr 1970), P. aeruginosa (Wang et al. 2006) A. calcoaceticus (Patel et al. 1976), or Rhodococcus sp. AN-22 (Matsumura et al. 2004). Varga and Neujahr (1970) suggested a correlation between substrate specificity and the affinity of iron to catechol 1,2-dioxygenases. They reported that dioxygenases with strongly bound iron had narrow substrate specificity and vice versa. Our results are at variance with this suggestions since the catechol 1,2-dioxygenase from strain KB2 has a narrow specificity and apparently weakly bound iron. The sensitivity of our enzyme ton the chelators may be connected with the untypical ligand (Gln-224) of iron in the active site of the dioxygenase (Fig. 3c).
In conclusion catechol 1,2-dioxygenase from S. maltophilia strain KB2 could be a useful tool in the production of cis,cis-muconic acid and its derivatives due to its high activity. The high activity of the enzyme in the presence of methylcatechols may enables it to be used to produce methyl derivatives of cis,cis-muconic acid. Moreover, the temperature and pH tolerance, and resistance to competitive inhibitors, may be desirable features of the catechol 1,2-dioxygenase from KB2 strain for industrial processes .