Wide substrate range for a candidate bioremediation enzyme isolated from Nocardioides sp. strain SG-4 G

Abstract

Narrow substrate ranges can impact heavily on the range of applications and hence commercial viability of candidate bioremediation enzymes. Here we show that an ester hydrolase from Nocardioides strain SG-4 G has potential as a bioremediation agent against various pollutants that can be detoxified by hydrolytic cleavage of some carboxylester, carbamate, or amide linkages. Previously we showed that a radiation-killed, freeze-dried preparation (ZimA) of this strain can rapidly degrade the benzimidazole fungicide carbendazim due to the activity of a specific ester hydrolase, MheI. Here, we report that ZimA also has substantial hydrolytic activity against phthalate diesters (dimethyl, dibutyl, and dioctyl phthalate), anilide (propanil and monalide), and carbamate ester (chlorpropham) herbicides under laboratory conditions. The reaction products are substantially less toxic, or inactive as herbicides, than the parent compounds. Tests of strain SG-4 G and Escherichia coli expressing MheI found they were also able to hydrolyse dimethyl phthalate, propanil, and chlorpropham, indicating that MheI is principally responsible for the above activities.

Keywords: biodegradation; bioremediation; enzyme; herbicides; plasticizers; substrate specificity.

Figure 1.

Degradation of dimethyl phthalate by ZimA, strain SG-4 G, and E. coli cells expressing the mheI gene: (A) Degradation of 0.130 mM dimethyl phthalate and production of monomethyl phthalate by 400 ppm ZimA; (B) Degradation of different concentrations of dimethyl phthalate by 400 ppm ZimA; (C) Degradation of 1.28 mM dimethyl phthalate by live cells of the strain SG-4 G; and (D) Degradation of 0.13 mM dimethyl phthalate by E. coli cells expressing mheI.

Figure 2.

Plots of degradation rates against substrate concentrations for the reactions of ZimA with (A) dimethyl phthalate, (B) propanil, (C) monalide, and (D) chlorpropham.

Figure 3.

Degradation of 54 μM dibutyl phthalate (A) and 26 μM dioctyl phthalate (B) by 400 ppm ZimA.

Figure 4.

Degradation of different concentrations of propanil (A) and monalide (B) by 800 ppm ZimA.

Figure 5.

Degradation of 46.8 μM chlorpropham by varying concentrations ZimA.

Figure 6.

Heat map-coded correlation matrix of amino acid similarity percentages for enzymes with activity against any of the phthalates, carbamates, amides found to be substrates for MheI here or in Pandey et al. (2010). Note that only one of the four MheI isolates other than the one herein from SG-4 G is shown because the rest were not biochemically characterized in detail. Abbreviations for substrates and accession numbers for enzymes are as per Supplementary Table S2. Clustal Omega 1.2.2 (mBed algorithm) was used for multiple protein sequence alignment and generating the identity matrix (Sievers and Higgins 2018).