Comprehensive genomic and transcriptomic analysis of polycyclic aromatic hydrocarbon degradation by a mycoremediation fungus, Dentipellis sp. KUC8613

Hongjae Park, Byoungnam Min, Yeongseon Jang, Jungyeon Kim, Anna Lipzen, Aditi Sharma, Bill Andreopoulos, Jenifer Johnson, Robert Riley, Joseph W. Spatafora, Bernard Henrissat, Kyoung Heon Kim, Igor V. Grigoriev, Jae Jin Kim, In-Geol Choi

Research output: Contribution to journalArticle

Abstract

The environmental accumulation of polycyclic aromatic hydrocarbons (PAHs) is of great concern due to potential carcinogenic and mutagenic risks, as well as their resistance to remediation. While many fungi have been reported to break down PAHs in environments, the details of gene-based metabolic pathways are not yet comprehensively understood. Specifically, the genome-scale transcriptional responses of fungal PAH degradation have rarely been reported. In this study, we report the genomic and transcriptomic basis of PAH bioremediation by a potent fungal degrader, Dentipellis sp. KUC8613. The genome size of this fungus was 36.71 Mbp long encoding 14,320 putative protein-coding genes. The strain efficiently removed more than 90% of 100 mg/l concentration of PAHs within 10 days. The genomic and transcriptomic analysis of this white rot fungus highlights that the strain primarily utilized non-ligninolytic enzymes to remove various PAHs, rather than typical ligninolytic enzymes known for playing important roles in PAH degradation. PAH removal by non-ligninolytic enzymes was initiated by both different PAH-specific and common upregulation of P450s, followed by downstream PAH-transforming enzymes such as epoxide hydrolases, dehydrogenases, FAD-dependent monooxygenases, dioxygenases, and glycosyl- or glutathione transferases. Among the various PAHs, phenanthrene induced a more dynamic transcriptomic response possibly due to its greater cytotoxicity, leading to highly upregulated genes involved in the translocation of PAHs, a defense system against reactive oxygen species, and ATP synthesis. Our genomic and transcriptomic data provide a foundation of understanding regarding the mycoremediation of PAHs and the application of this strain for polluted environments.

Original languageEnglish
JournalApplied Microbiology and Biotechnology
DOIs
Publication statusAccepted/In press - 2019 Jan 1

Fingerprint

Polycyclic Aromatic Hydrocarbons
Fungi
Enzymes
dimethylaniline monooxygenase (N-oxide forming)
Epoxide Hydrolases
Genome Size
Dioxygenases
Environmental Biodegradation
Metabolic Networks and Pathways
Glutathione Transferase
Genes
Reactive Oxygen Species
Oxidoreductases
Up-Regulation
Adenosine Triphosphate

Keywords

  • Dentipellis sp. KUC8613
  • Genomics
  • Mycoremediation
  • PAH (polycyclic aromatic hydrocarbon)
  • Transcriptomics
  • White rot fungus

ASJC Scopus subject areas

  • Biotechnology
  • Applied Microbiology and Biotechnology

Cite this

Comprehensive genomic and transcriptomic analysis of polycyclic aromatic hydrocarbon degradation by a mycoremediation fungus, Dentipellis sp. KUC8613. / Park, Hongjae; Min, Byoungnam; Jang, Yeongseon; Kim, Jungyeon; Lipzen, Anna; Sharma, Aditi; Andreopoulos, Bill; Johnson, Jenifer; Riley, Robert; Spatafora, Joseph W.; Henrissat, Bernard; Kim, Kyoung Heon; Grigoriev, Igor V.; Kim, Jae Jin; Choi, In-Geol.

In: Applied Microbiology and Biotechnology, 01.01.2019.

Research output: Contribution to journalArticle

Park, Hongjae ; Min, Byoungnam ; Jang, Yeongseon ; Kim, Jungyeon ; Lipzen, Anna ; Sharma, Aditi ; Andreopoulos, Bill ; Johnson, Jenifer ; Riley, Robert ; Spatafora, Joseph W. ; Henrissat, Bernard ; Kim, Kyoung Heon ; Grigoriev, Igor V. ; Kim, Jae Jin ; Choi, In-Geol. / Comprehensive genomic and transcriptomic analysis of polycyclic aromatic hydrocarbon degradation by a mycoremediation fungus, Dentipellis sp. KUC8613. In: Applied Microbiology and Biotechnology. 2019.
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AU - Kim, Jungyeon

AU - Lipzen, Anna

AU - Sharma, Aditi

AU - Andreopoulos, Bill

AU - Johnson, Jenifer

AU - Riley, Robert

AU - Spatafora, Joseph W.

AU - Henrissat, Bernard

AU - Kim, Kyoung Heon

AU - Grigoriev, Igor V.

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