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Biodegradation

, Volume 19, Issue 6, pp 859–881 | Cite as

Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1

  • Seong-Jae Kim
  • Ohgew Kweon
  • Richard C. Jones
  • Ricky D. Edmondson
  • Carl E. CernigliaEmail author
Original Paper

Abstract

Mycobacterium vanbaalenii PYR-1 is well known for its ability to degrade a wide range of high-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs). The genome of this bacterium has recently been sequenced, allowing us to gain insights into the molecular basis for the degradation of PAHs. The 6.5 Mb genome of PYR-1 contains 194 chromosomally encoded genes likely associated with degradation of aromatic compounds. The most distinctive feature of the genome is the presence of a 150 kb major catabolic region at positions 494 ~ 643 kb (region A), with an additional 31 kb region at positions 4,711 ~ 4,741 kb (region B), which is predicted to encode most enzymes for the degradation of PAHs. Region A has an atypical mosaic structure made of several gene clusters in which the genes for PAH degradation are complexly arranged and scattered around the clusters. Significant differences in the gene structure and organization as compared to other well-known aromatic hydrocarbon degraders including Pseudomonas and Burkholderia were revealed. Many identified genes were enriched with multiple paralogs showing a remarkable range of diversity, which could contribute to the wide variety of PAHs degraded by M. vanbaalenii PYR-1. The PYR-1 genome also revealed the presence of 28 genes involved in the TCA cycle. Based on the results, we proposed a pathway in which HMW PAHs are degraded into the β-ketoadipate pathway through protocatechuate and then mineralized to CO2 via TCA cycle. We also identified 67 and 23 genes involved in PAH degradation and TCA cycle pathways, respectively, to be expressed as proteins.

Keywords

Degradation Genomic analysis Mycobacterium vanbaalenii PYR-1 Polycyclic aromatic hydrocarbons Proteome analysis 

Abbreviations

CYPs

Cytochrome P450 monooxygenases

HMW

High-molecular-weight

JGI

Joint Genome Institute

KEGG

Kyoto Encyclopedia of Genes and Genomes

ORFs

Open reading frames

PAHs

Polycyclic aromatic hydrocarbons

RHOs

Ring-hydroxylating oxygenases

Notes

Acknowledgments

We thank Robin L. Stingley and Ashraf A. Khan for critical review of the manuscript and Thomas D. Yun for graphical assistance. The authors acknowledge Charles D. Miller and Ronald C. Sims at the Utah State University and the staff of the Joint Genome Institute for their efforts with the genome sequencing of M. vanbaalenii PYR-1. This work was supported by an appointment to the Postgraduate Research Program at the National Center for Toxicological Research administered by the Oak Ridge Institute for Science and Education through an interagency agreement between the U. S. Department of Energy and the U. S. Food and Drug Administration.

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Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Seong-Jae Kim
    • 1
  • Ohgew Kweon
    • 1
  • Richard C. Jones
    • 2
    • 3
  • Ricky D. Edmondson
    • 2
    • 4
  • Carl E. Cerniglia
    • 1
    Email author
  1. 1.Division of MicrobiologyNational Center for Toxicological Research/U.S. FDAJeffersonUSA
  2. 2.Division of Systems ToxicologyNational Center for Toxicological Research/U.S. FDAJeffersonUSA
  3. 3.NextGen/PRSAnn ArborUSA
  4. 4.Myeloma Institute for Research and TherapyUniversity of Arkansas for Medical SciencesLittle RockUSA

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