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Biodegradation

, Volume 24, Issue 6, pp 741–752 | Cite as

A global proteome study of Mycobacterium gilvum PYR-GCK grown on pyrene and glucose reveals the activation of glyoxylate, shikimate and gluconeogenetic pathways through the central carbon metabolism highway

  • Abimbola Comfort Badejo
  • Chi-Won Choi
  • Adegoke Olugboyega Badejo
  • Kyung-Hoon Shin
  • Jung-Ho Hyun
  • Yeol-Gyun Lee
  • Seung-il Kim
  • Kang-Sik Park
  • Sang Hoon Kim
  • Kyoung Hwa Jung
  • Young-Ho Chung
  • Young Gyu Chai
Original Paper

Abstract

Various hydrocarbons have been released into the environment as a result of industrialization. An effective way of removing these materials without further environmental contamination is microbial bioremediation. Mycobacterium gilvum PYR-GCK, a bacteria isolated from a PAH polluted estuary, was studied using comparative shotgun proteomics to gain insight on its molecular activity while using pyrene and glucose as sole carbon and energy sources. Based on annotated genomic information, a confirmation analysis was first performed to confirm its pyrene degradation activity, using gas chromatography–mass spectrometry technology. One dimensional gel electrophoresis and liquid chromatography–mass spectrometry technologies employed in the proteomics analysis revealed the expression of pyrene degrading gene products along with upregulated expression of proteins functioning in the glyoxylate and shikimate pathways, in the pyrene-induced cells. The study also revealed the pathway of pyrene degraded intermediates, via partial gluconeogenesis, into the pentose phosphate pathway to produce precursors for nucleotides and amino acids biosynthesis.

Keywords

Polycyclic aromatic hydrocarbons Proteomics Shikimate Glyoxylate Mycobacterium gilvum PYR-GCK 

Notes

Acknowledgments

This work was supported by the Development of Biohydrogen Production Technology using Hyperthermophilic Archaea program and the Marine and Extreme Genome Research Center program of the Ministry of Land, Transport, and Maritime Affairs, a KBSI grant (K32403) to Y.H.C., and the National Research Foundation of Korea Grant funded by the Korean Government (No. 2012-0009212 to Y.G.C).

Supplementary material

10532_2013_9622_MOESM1_ESM.pdf (231 kb)
Online Resource 1: The gas chromatogram of the extracted pyrene residue at a 0 h (day 0) and b 48 h (day 2) from the pyrene-induced Mycobacterium gilvum PYR-GCK culture. Quantification was based on the integration of FID-peak areas of absolute pyrene identification and 2-nanodecanone was used as an injected internal reference standard. Supplementary material 1 (PDF 231 kb)
10532_2013_9622_MOESM2_ESM.pdf (245 kb)
Online Resource 2: Mass-fragment spectra of the degraded pyrene substrate showing metabolites identification of a phthalic acid and b 1,10-phenanthrene dicarboxylic acid in Mycobacterium gilvum PYR-GCK. Relative identification of pyrene metabolites were accomplished based on the library similarity search on the GC/MS software program as well as metabolites structures and fragment patterns from published papers. Supplementary material 2 (PDF 244 kb)
10532_2013_9622_MOESM3_ESM.pdf (1.6 mb)
Online Resource 3: List of all identified proteins in Mycobacterium gilvum PYR-GCK by Mascot database search. Gene locus tags are numbers assigned to each gene in the annotated genome sequence. Proteins were identified and normalized based on NSAF, PAF and emPAI (explained in “Materials and methods”). Significantly regulated proteins are based on quantification in at least 2 of 3 biological replicates, a mean regulation factor ratio of <−0.5 or ≥2 and a p value of ≤0.05 (in bold fonts). Parameters (ratio and p value) with glucose or pyrene written signify samples with binary expression in the corresponding substrate induced samples. All values are acquired from triplicate analyses. Supplementary material 3 (PDF 1625 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Abimbola Comfort Badejo
    • 1
  • Chi-Won Choi
    • 2
  • Adegoke Olugboyega Badejo
    • 3
  • Kyung-Hoon Shin
    • 3
  • Jung-Ho Hyun
    • 3
  • Yeol-Gyun Lee
    • 2
  • Seung-il Kim
    • 2
  • Kang-Sik Park
    • 4
  • Sang Hoon Kim
    • 1
  • Kyoung Hwa Jung
    • 1
  • Young-Ho Chung
    • 2
  • Young Gyu Chai
    • 1
  1. 1.Division of Molecular and Life SciencesHanyang University (ERICA)AnsanKorea
  2. 2.Division of Life ScienceKorea Basic Science InstituteDaejeonKorea
  3. 3.Department of Environmental and Marine ScienceHanyang University (ERICA)AnsanKorea
  4. 4.Department of Physiology, School of MedicineKyunghee UniversitySeoulKorea

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