Sequestration of a highly reactive intermediate in an evolving pathway for degradation of pentachlorophenol

Edited by Gregory A. Petsko, Brandeis University, Waltham, MA, and approved April 18, 2013 (received for review August 21, 2012)
May 15, 2013
110 (24) E2182-E2190

Significance

Microbes in contaminated environments often evolve new metabolic pathways for detoxification or degradation of pollutants. In some cases, intermediates in newly evolving pathways are more toxic than the initial compound. The initial step in the degradation of pentachlorophenol by Sphingobium chlorophenolicum generates a particularly toxic intermediate, tetrachlorobenzoquinone (TCBQ). This paper describes how the bacterium is protected from the toxic effects of TCBQ. In the presence of tetrachlorobenzoquinone reductase, TCBQ produced by pentachlorophenol hydroxylase is sequestered until it is reduced to the less toxic tetrachlorohydroquinone.

Abstract

Microbes in contaminated environments often evolve new metabolic pathways for detoxification or degradation of pollutants. In some cases, intermediates in newly evolved pathways are more toxic than the initial compound. The initial step in the degradation of pentachlorophenol by Sphingobium chlorophenolicum generates a particularly reactive intermediate; tetrachlorobenzoquinone (TCBQ) is a potent alkylating agent that reacts with cellular thiols at a diffusion-controlled rate. TCBQ reductase (PcpD), an FMN- and NADH-dependent reductase, catalyzes the reduction of TCBQ to tetrachlorohydroquinone. In the presence of PcpD, TCBQ formed by pentachlorophenol hydroxylase (PcpB) is sequestered until it is reduced to the less toxic tetrachlorohydroquinone, protecting the bacterium from the toxic effects of TCBQ and maintaining flux through the pathway. The toxicity of TCBQ may have exerted selective pressure to maintain slow turnover of PcpB (0.02 s−1) so that a transient interaction between PcpB and PcpD can occur before TCBQ is released from the active site of PcpB.

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Data Availability

Data deposition: The sequences for the previously unsequenced PcpD proteins reported in this paper have been deposited in the GenBank database [accession nos. JX514946 (Sphingobium chlorophenolicum sp. RA2), JX514945 (Sphingobium chlorophenolicum ATCC 33790), and JX514944 (Novosphingobium lentum)].

Acknowledgments

This work was funded by National Institutes of Health Grant GM078554 (to S.D.C.).

Supporting Information

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Supporting Information

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Information & Authors

Information

Published in

Go to Proceedings of the National Academy of Sciences
Go to Proceedings of the National Academy of Sciences
Proceedings of the National Academy of Sciences
Vol. 110 | No. 24
June 11, 2013
PubMed: 23676275

Classifications

Data Availability

Data deposition: The sequences for the previously unsequenced PcpD proteins reported in this paper have been deposited in the GenBank database [accession nos. JX514946 (Sphingobium chlorophenolicum sp. RA2), JX514945 (Sphingobium chlorophenolicum ATCC 33790), and JX514944 (Novosphingobium lentum)].

Submission history

Published online: May 15, 2013
Published in issue: June 11, 2013

Keywords

  1. biodegradation
  2. molecular evolution
  3. channeling
  4. quinone reductase

Acknowledgments

This work was funded by National Institutes of Health Grant GM078554 (to S.D.C.).

Notes

This article is a PNAS Direct Submission.

Authors

Affiliations

Itamar Yadid1
Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309
Johannes Rudolph1
Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309
Klara Hlouchova
Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309
Present address: Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, Prague, Czech Republic.
Shelley D. Copley3 [email protected]
Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309

Notes

3
To whom correspondence should be addressed. E-mail: [email protected].
Author contributions: I.Y., J.R., and S.D.C. designed research; I.Y., J.R., and K.H. performed research; I.Y., J.R., and S.D.C. analyzed data; I.Y., J.R., and S.D.C. wrote the paper.
1
I.Y. and J.R contributed equally to this work.

Competing Interests

The authors declare no conflict of interest.

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    Sequestration of a highly reactive intermediate in an evolving pathway for degradation of pentachlorophenol
    Proceedings of the National Academy of Sciences
    • Vol. 110
    • No. 24
    • pp. 9615-10046

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