Skip to main content
SpringerLink
Log in

Identification of new enzymes potentially involved in anaerobic naphthalene degradation by the sulfate-reducing enrichment culture N47

  • Original Paper
  • Published:
Archives of Microbiology Aims and scope Submit manuscript

Abstract

The sulfate-reducing highly enriched culture N47 is capable to anaerobically degrade naphthalene, 2-methylnaphthalene, and 2-naphthoic acid. A proteogenomic investigation was performed to elucidate the initial activation reaction of anaerobic naphthalene degradation. This lead to the identification of an alpha-subunit of a carboxylase protein that was two-fold up-regulated in naphthalene-grown cells compared to 2-methylnaphthalene-grown cells. The putative naphthalene carboxylase subunit showed 48% similarity to the anaerobic benzene carboxylase from an iron-reducing, benzene-degrading culture and 45% to alpha-subunit of phenylphosphate carboxylase of Aromatoleum aromaticum EbN1. A gene for the beta-subunit of putative naphthalene carboxylase was located nearby on the genome and was expressed with naphthalene. Similar to anaerobic benzene carboxylase, there were no genes for gamma- and delta-subunits of a putative carboxylase protein located on the genome which excludes participation in degradation of phenolic compounds. The genes identified for putative naphthalene carboxylase subunits showed only weak similarity to 4-hydroxybenzoate decarboxylase excluding ATP-independent carboxylation. Several ORFs were identified that possibly encode a 2-naphthoate-CoA ligase, which is obligate for activation before the subsequent ring reduction by naphthoyl-CoA reductase. One of these ligases was exclusively expressed on naphthalene and 2-naphthoic acid and might be the responsible naphthoate-CoA-ligase.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Abu Laban N, Selesi D, Rattei T, Tischler P, Meckenstock RU (2010) Identification of enzymes involved in anaerobic benzene degradation by a strictly anaerobic iron-reducing enrichment culture. Environ Microbiol 12:2783–2796

    PubMed  CAS  Google Scholar 

  • Altschul SF et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

  • Annweiler E et al (2000) Anaerobic degradation of 2-methylnaphthalene by a sulfate-reducing enrichment culture. Appl Environ Microb 66:5329–5333

    Article  CAS  Google Scholar 

  • Bergmann FD, Selesi D, Weinmaier T, Tischler P, Rattei T, Meckenstock RU (2010) Genomic insights into the metabolic potential of the polycyclic aromatic hydrocarbon degrading sulphate-reducing Deltaproteobacterium N47. Environ Microbiol

  • Boll M, Fuchs G, Heider J (2002) Anaerobic oxidation of aromatic compounds and hydrocarbons. Curr Opin Chem Biol 6:604–611

    Article  PubMed  CAS  Google Scholar 

  • Cline JD (1969) Spectrophotometric determination of hydrogen sulfide in natural waters. Limnol Oceanogr 14:454–458

    Article  CAS  Google Scholar 

  • Galushko A, Minz D, Schink B, Widdel F (1999) Anaerobic degradation of naphthalene by a pure culture of a novel type of marine sulphate-reducing bacterium. Environ Microbiol 1:415–420

    Article  PubMed  CAS  Google Scholar 

  • Gibson J, Dispensa M, Fogg GC, Evans DT, Harwood CS (1994) 4-Hydroxybenzoate-coenzyme A ligase from Rhodopseudomonas palustris: purification, gene sequence, and role in anaerobic degradation. J Bacteriol 176:634–641

    PubMed  CAS  Google Scholar 

  • Habe H, Omori T (2003) Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria. Biosci Biotech Bioch 67:225–243

    Article  CAS  Google Scholar 

  • He Z, Wiegel J (1995) Purification and characterization of an oxygen-sensitive reversible 4-hydroxybenzoate decarboxylase from Clostridium hydroxybenzoicum. Eur J Biochem 229:77–82

    Article  PubMed  CAS  Google Scholar 

  • Keller A, Nesvizhskii AI, Kolker E, Aebersold R (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 74:5383–5392

    Article  PubMed  CAS  Google Scholar 

  • Leuthner B et al (1998) Biochemical and genetic characterization of benzylsuccinate synthase from Thauera aromatica: a new glycyl radical enzyme catalysing the first step in anaerobic toluene metabolism. Mol Microbiol 28:615–628

    Article  PubMed  CAS  Google Scholar 

  • Lueders T, Kindler R, Miltner A, Friedrich MW, Kaestner M (2006) Identification of bacterial micropredators distinctively active in a soil microbial food web. Appl Environ Microb 72:5342–5348

    Article  CAS  Google Scholar 

  • Meckenstock RU, Annweiler E, Michaelis W, Richnow HH, Schink B (2000) Anaerobic naphthalene degradation by a sulfate-reducing enrichment culture. Appl Environ Microb 66:2743–2747

    Article  CAS  Google Scholar 

  • Musat F et al (2009) Anaerobic degradation of naphthalene and 2-methylnaphthalene by strains of marine sulfate-reducing bacteria. Environ Microbiol 11:209–219

    Article  PubMed  CAS  Google Scholar 

  • Muyzer G, Teske A, Wirsen C, Jannasch H (1995) Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol 164:165–172

    Article  PubMed  CAS  Google Scholar 

  • Nesvizhskii AI, Keller A, Kolker E, Aebersold R (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 75:4646–4658

    Article  PubMed  CAS  Google Scholar 

  • Rabus R et al (2005) The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Arch Microbiol 183:27–36

    Article  PubMed  CAS  Google Scholar 

  • Rappsilber J, Siniossoglou S, Hurt EC, Mann M (2000) A generic strategy to analyze the spatial organization of multi-protein complexes by cross-linking and mass spectrometry. Anal Chem 72:267–275

    Article  PubMed  CAS  Google Scholar 

  • Rockne KJ, Chee-Sanford JC, Sanford RA, Hedlund BP, Staley JT, Strand SE (2000) Anaerobic naphthalene degradation by microbial pure cultures under nitrate-reducing conditions. Appl Environ Microb 66:1595–1601

    Article  CAS  Google Scholar 

  • Safinowski M, Meckenstock RU (2004) Enzymatic reactions in anaerobic 2-methylnaphthalene degradation by the sulphate-reducing enrichment culture N47. FEMS Microbiol Lett 240:99–104

    Article  PubMed  CAS  Google Scholar 

  • Safinowski M, Meckenstock RU (2006) Methylation is the initial reaction in anaerobic naphthalene degradation by a sulfate-reducing enrichment culture. Environ Microbiol 8:347–352

    Article  PubMed  CAS  Google Scholar 

  • Schuhle K, Fuchs G (2004) Phenylphosphate carboxylase: a new C-C lyase involved in anaerobic in phenol metabolism in Thauera aromatica. J Bacteriol 186:4556–4567

    Article  PubMed  Google Scholar 

  • Selesi D et al (2010) Combined genomic and proteomic approaches identify gene clusters involved in anaerobic 2-methylnaphthalene degradation in the sulfate-reducing enrichment culture N47. J Bacteriol 192:295–306

    Article  PubMed  CAS  Google Scholar 

  • Ting L, Cowley MJ, Hoon SL, Guilhaus M, Raftery MJ, Cavicchioli R (2009) Normalization and statistical analysis of quantitative proteomics data generated by metabolic labeling. Mol Cell Proteomics 8:2227–2242

    Article  PubMed  CAS  Google Scholar 

  • Walter MC et al (2009) PEDANT covers all complete RefSeq genomes. Nucleic Acids Res 37:D408–D411

    Article  PubMed  CAS  Google Scholar 

  • Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703

    PubMed  CAS  Google Scholar 

  • Wu LF, Han DK (2006) Overcoming the dynamic range problem in mass spectrometry-based shotgun proteomics. Expert Rev Proteomic 3:611–619

    Article  CAS  Google Scholar 

  • Zehr BD, Savin TJ, Hall RE (1989) A one-step, low background Coomassie staining procedure for polyacrylamide gels. Anal Biochem 182:157–159

    Article  PubMed  CAS  Google Scholar 

  • Zhang XM, Young LY (1997) Carboxylation as an initial reaction in the anaerobic metabolism of naphthalene and phenanthrene by sulfidogenic consortia. Appl Environ Microb 63:4759–4764

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute of Groundwater Ecology, Helmholtz Zentrum München—German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany

    Franz D. Bergmann, Draženka Selesi & Rainer U. Meckenstock

Authors
  1. Franz D. Bergmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Draženka Selesi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rainer U. Meckenstock
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Rainer U. Meckenstock.

Additional information

Communicated by Joerg Overmann.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Bergmann, F.D., Selesi, D. & Meckenstock, R.U. Identification of new enzymes potentially involved in anaerobic naphthalene degradation by the sulfate-reducing enrichment culture N47. Arch Microbiol 193, 241–250 (2011). https://doi.org/10.1007/s00203-010-0667-4

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00203-010-0667-4

Keywords

Search

Navigation