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pdoA2 from Mycobacterium sp. strain 6PY1

Encodes phenanthrene ring-hydroxylating oxygenase α-subunit. Presumably catalyzes as a complex with pdoB2, phtAc and phtAd the oxidation of phenanthrene-4-carboxylate to cis-3,4-dihydroxy-phenanthrene-4-carboxylate. This is the fifth step in pyrene biodegradation. [1]

Background

It is well-established that phtAc and phtAd together function as an electron transport chain, facilitating electron transfer from NADH [1].This system is crucial for supplying electrons to various dioxygenase systems, which are involved in the reduction of polycyclic aromatic hydrocarbons (PAHs). One such complex with dioxygenase activity is formed by nidA and nidBtogether with phtAc and phtAd, capable of degrading pyrene into cis-4,5-dihydroxy-4,5-dihydropyrene [2].

In this project, our complex of interest is formed by the ring-hydroxylating dioxygenase system, composed by pdoA2 and pdoB2 . Together with phtAcAd, these components aggregate to form a complex that exhibits dioxygenase activity [4–6]. This complex is capable of converting phenanthrene-4-carboxylate, an intermediate product of pyrene degradation, into cis-3,4-dihydroxy-phenanthrene-4-carboxylate, see Figure 1 [5, 6]. Given this reaction’s importance in pyrene degradation, we opted to conduct a more detailed characterization. The components of the electron transport chain, phtAc a ferredoxin and ferredoxin reductase phtAd, were produced and purified to elucidate their kinetic parameters. Subsequently, we aimed to analyze the complex formation with pdoA2B2 through HPLC analysis.

Enzyme production and purification

Enzyme coding sequences were cloned into pQE bacterial expression vector with a N-terminal, hexahistidine tag. Proteins were expressed in E. coli BL21 (DE3). Main cultures were incubated at 37°C until an OD600 of 0.5 was reached. Subsequently, cultures were induced with a final concentration of 0.5 mM IPTG and incubated overnight at 30°C. Purification was performed using Immobilized Metal Affinity Chromatography (IMAC). Both production and purification samples were analyzed via SDS-PAGE and Coomassie staining (data not shown). Enzyme concentration was determined using the Bradford Assay [6]. The finaL protein yield was 79.4 µM.

Activity assay coupled with HPLC analysis

We successfully characterized and demonstrated the activity of phtAc and phtAd both individually and as a complex. This complex functions as an electron carrier for pdoA2B2 [2–4]. The subsequent step involved conducting an activity assay in conjunction with HPLC analysis with the aim to evaluate the function of pdoA2B2 both independently and in complex with phtAcAd, forming a tetramer.

Method

Initially, the activity assay was conducted, wherein the enzymes were incubated at 30°C for approximately 15 to 20 minutes, both in the presence and absence of NADH to examine the effect of NADH on enzymatic aggregation. Subsequently, phenanthrene-4-carboxylate (P4C) was added to initiate the reaction. The reaction mixture was then incubated for 30 minutes at 30°C, after which the reaction was terminated by the addition of 100% methanol. Following this, HPLC analysis was performed using a Zorbax SB-C18 column, employing an acetonitrile/water gradient at a flow rate of 0.4 ml/min, with the column oven maintained at room temperature. The gradient elution program commenced with an initial mobile phase of 60:40 (v/v) acetonitrile to water, transitioning linearly to 100% acetonitrile over 14 minutes, followed by a return to the initial phase (60:40) after 5 minutes. The total duration for each analysis was 35 minutes. For the negative control, an assay was conducted using denatured enzymes, achieved by heating the enzymes at 95°C for 10 minutes. Peaks were analyzed at 270nm absorbance.

Results

Initial activity assays were performed solely with pdoA2 and pdoB2 to form a dimer, thereby validating their enzymatic activity and evaluating their aggregation characteristics. Monomers were incubated together for aggregation in the presence and absence of NADH to determine whether NADH, as a cofactor, influences the aggregation process.
The efficacy of the reaction was assessed by measuring the absorbance of phenanthrene-4-carboxylate (P4C) and NADH using HPLC. The area under the resulting peaks corresponding to the levels of P4C and NADH was determined, enabling a comparative analysis of the consumption of P4C and NADH against established standards and between the samples. In this context, phenanthrene-4-carboxylate consumption refers to the extent of P4C degradation, as indicated by a reduction in peak area compared to the standard. In the absence of additional samples with different concentrations, it is not possible to quantify the remaining P4C in the samples. The only conclusion that can be drawn is whether P4C has been degraded, as evidenced by the decrease in the area of the corresponding peak; this applies also to NADH. Furthermore, to eliminate potential statistical errors in the assessment of our results, we employed triplicate measurements for each sample and calculated their averages. The results are presented in Figure 2. Results indicated that the assays in which NADH was added prior to aggregation exhibited enhanced P4C degradation and, correspondingly, increased NADH consumption compared to the assays where NADH was added after aggregation. However, the observed NADH consumption was relatively low, which may be attributed to the absence of the electron carrier dimer (phtAcAd) in the sample, thereby limiting NADH consumption.

Considering the initial results, the analysis of the tetramer aggregation process and the degradation of phenanthrene-4-carboxylat was conducted by introducing NADH prior to the aggregation process.

Degradation of phenanthrene-4-carboxylat by enzyme complex with dioxygenase activity using NADH as a cofactor
The presence of the functional enzyme complex with dioxygenase activity is anticipated to result in a reduction in the quantity of phenanthrene-4-carboxylate. This reduction can be quantified by determining the decrease in the area of the corresponding peak in comparison to the standard. Given the unknown stoichiometry of this enzyme complex, we conducted assays utilizing two distinct stoichiometric ratios. The first assay employed a 1:1 stoichiometry of all monomers, while the second utilized a ratio of pdoA2¹:pdoB2¹:phtAc³:phtAd¹. This latter stoichiometry was selected based on previous kinetic analyses of phtAc, which were performed with a ratio of three phtAc molecules to one phtAd for determining kinetic parameters. [5] This ratio was employed in the present assays to assess its influence on the degradation of phenanthrene-4-carboxylate and to determine whether the presence of three equivalents phtAc enhanced the efficiency of the electron transfer process, thereby accelerating the breakdown of phenanthrene-4-carboxylate. However, results showed (see Figure 3) that the breakdown of phenanthrene-4-carboxylat was slightly more efficient with the 1:1 ratio of the monomers; this could suggest that a higher ratio of phtAc does not enhance the electron transfer process. And that the complex with 1:1 ratio of all enzymes aggregates better.

To confirm the aggregation of the enzyme complex and the successful degradation of P4C by this complex, negative controls were prepared. For this, assays were prepared with denatured enzymes with the stoichiometries described above. Results showed (see Figure 3) that the peak area of P4C within these assays was higher in comparison with the assays with the active enzyme complex. The comparison of these results indicates that the enzyme complex was successfully formed and demonstrated the capacity to degrade P4C.

Another negative control was conducted by excluding any enzymes from the assay. In comparison to samples containing denatured enzymes, the results showed a reduced peak area in the peak corresponding to phenanthrene-4-carboxylate, suggesting either a diminished quantity of P4C in the sample or its degradation. However, the possibility of cross-reactivity with other components in the assay can be discounted, as such interactions would also manifest in the other negative controls. This observation indicates the presence of an independent source of error. Potential issues may involve the unintentional introduction of enzymes or inadequate substrate concentration. The presence of enzymes in the assay can be corroborated by taking into consideration the amount of NADH; notably, the peak area of NADH in this sample was diminished suggesting the possibility that a reaction has taken place, and the results are more consistent with those obtained from the assay conducted with a 1:3 enzyme ratio (see Figure 3). While numerous errors could have arisen, a systematic issue such as cross-reactivity, which would render the enzyme ineffective, can be dismissed by comparing the sample to those with non-functional enzymes.

Moreover, as anticipated, the samples containing the active enzyme complex demonstrated a decrease in the peak area associated with NADH relative to the standard (see Figure 3). This finding corroborates the functionality of the electron carrier dimer, which collaborates with pdoA2B2 in the degradation of P4C. In contrast, the assay involving denatured enzymes at a 1:1 ratio revealed no consumption of NADH, indicating the absence of any reaction.

However, the results of NADH consumption from the assay involving denatured enzymes, utilizing three equivalents of phtAc in conjunction with a 1:1 ratio of the other enzymes, demonstrate a reduction in NADH consumption, as evidenced by the diminished area of the corresponding peak relative to the standard. This observation indicates the presence of an independent source of error, as the other assay performed with denatured enzymes shows no NADH consumption. Potential issues may include insufficient NADH concentration. If the NADH concentration was low, degradation could have occurred over time, as the activity assays were conducted days prior to the HPLC analysis. The thawing process and exposure of the sample to temperature fluctuations may have contributed to NADH degradation due to its inherent instability. Additionally, the possibility of incomplete denaturation should be considered. If the enzymes were not fully denatured during the assay, residual active enzyme could remain, resulting in NADH consumption. The denaturation conditions may not have been adequate to completely inactivate the enzymes. This is further supported by the observation that P4C consumption was slightly lower in comparison to the sample with denatured enzymes with the 1:1 ratio.

Conclusion

In conclusion, the enzyme complex with dioxygenase activity demonstrated its ability to degrade phenanthrene-4-carboxylate (P4C), with slightly greater efficiency observed in the assay utilizing a 1:1 ratio of monomers compared to the 1:3 ratio of phtAc to pdoA2:pdoB2:phtAd. This suggests that a higher ratio of phtAc does not enhance electron transfer efficiency. Negative controls, including assays with denatured enzymes and no enzymes, confirmed that the active enzyme complex was responsible for P4C degradation, while the reduction in NADH in some denatured enzyme assays points to possible errors, such as NADH degradation or incomplete enzyme denaturation. Further assays with stricter controls are needed to confirm these findings and minimize potential sources of error.

Sequence and Features

References

[1] S.-J. Kim, O. Kweon, R. C. Jones, J. P. Freeman, R. D. Edmondson, and C. E. Cerniglia, "Complete and integrated pyrene degradation pathway in Mycobacterium vanbaalenii PYR-1 based on systems biology," Journal of bacteriology, vol. 189, no. 2, pp. 464–472, 2007, doi: 10.1128/JB.01310-06.
[2] C. Pagnout, G. Frache, P. Poupin, B. Maunit, J.-F. Muller, and J.-F. Férard, "Isolation and characterization of a gene cluster involved in PAH degradation in Mycobacterium sp. strain SNP11: expression in Mycobacterium smegmatis mc(2)155," Research in microbiology, vol. 158, no. 2, pp. 175–186, 2007, doi: 10.1016/j.resmic.2006.11.002.
[3] K. Yuan et al., "Transcriptional response of Mycobacterium sp. strain A1-PYR to multiple polycyclic aromatic hydrocarbon contaminations," Environmental pollution (Barking, Essex : 1987), vol. 243, Pt B, pp. 824–832, 2018, doi: 10.1016/j.envpol.2018.09.001.
[4] S. Krivobok, S. Kuony, C. Meyer, M. Louwagie, J. C. Willison, and Y. Jouanneau, "Identification of pyrene-induced proteins in Mycobacterium sp. strain 6PY1: evidence for two ring-hydroxylating dioxygenases," Journal of bacteriology, vol. 185, no. 13, pp. 3828–3841, 2003, doi: 10.1128/jb.185.13.3828-3841.2003.
[5] Y. Wu, Y. Xu, and N. Zhou, "A newly defined dioxygenase system from Mycobacterium vanbaalenii PYR-1 endowed with an enhanced activity of dihydroxylation of high-molecular-weight polyaromatic hydrocarbons," Front. Environ. Sci. Eng., vol. 14, no. 1, 2020, doi: 10.1007/s11783-019-1193-5.
[6] M. M. Bradford, "A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding," Analytical biochemistry, vol. 72, pp. 248–254, 1976, doi: 10.1006/abio.1976.9999.