Skip to main content
SpringerLink
Log in

Investigating the specificity of regulators of degradation of hydrocarbons and hydrocarbon-based compounds using structure-activity relationships

  • Published:
Biodegradation Aims and scope Submit manuscript

Abstract

Microbial biosensors which have genes forbioluminescence coupled to genes that controlhydrocarbon degradation pathways can be used asreporters on the specificity of regulation of thosepathways. Structure-activity relationships can be usedto discover what governs that specificity, and canalso be used to separate compounds into differentgroups depending on mode of action. Published data forfour different bioluminescent biosensors, reporting ontoluene (two separate biosensors), isopropylbenzene,and octane, were analyzed to developstructure-activity relationships between biologicalresponse and physical/chemical properties.Good QSARs (quantitative structure-activityrelationships) were developed for three out of thefour biosensors, with between 88 and 100 per cent ofthe variance explained. Parameters found to beimportant in controlling regulator specificity werehydrophobicity, lowest unoccupied molecular orbitalenergies, and molar volume. For one of the biosensors,it was possible to show that the biological responseto chemicals tested fell into three separate classes(non-hydrocarbons, aliphatic hydrocarbons, andaromatic hydrocarbons). A statistically significantQSAR based on hydrophobicity was developed for thefourth biosensor, but was poor in comparison to theother three (44 per cent variance explained).

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

Similar content being viewed by others

References

  • Abril MA, Michan C, Timmis KN & Ramos JL (1989) Regulator and enzyme specificities of the TOL plasmid-encoded upper pathway for degradation of aromatic hydrocarbons and expansion of the substrate range of the pathway. J. Bacteriol. 171: 6782–6790

    Google Scholar 

  • Aoki H, Kimura T, Habe H, Yamane H, Kodama T & Omori T (1996) Cloning, nucleotide sequence, and characterization of the genes encoding enzymes involved in the degradation of cumene to 2-hydroxy-6-oxo-7-methylocta-2,4-dienoic acid in Pseudomonas fluorescens IP01. Journal Of Fermentation and Bioengineering 81: 187–196

    Google Scholar 

  • Applegate BM, Kehrmeyer SR & Sayler GS (1998) A chromosomally-based tod-luxCDABE whole-cell reporter for benzene, toluene, ethylbenzene, and xylene (BTEX) sensing. Appl. Environ. Microbiol. 64: 2730–2735

    Google Scholar 

  • Atlas RM, Sayler GS, Burlage R & Bej AK (1992) Molecular approaches for environmental monitoring of microorganisms. Biotechniques 12: 706–717

    Google Scholar 

  • Barkay T, Nazaret S & Jeffrey W (1995) Degradative genes in the environment. In: Young LY & Cerniglia CE (Eds) Microbial Transformation and Degradation of Toxic Organic Chemicals (pp. 545–577). Wiley-Liss, New York

    Google Scholar 

  • Belkin S, Smulski DR, Dadon S, Vollmer AC, Van Dyk TK & LaRossa RA (1997) A panel of stress-responsive luminous bacteria for the detection of selected classes of toxicants. Wat. Res. 31: 3009–3016

    Google Scholar 

  • Cronin MTD & Dearden JC (1995) QSAR in toxicology. 1. Prediction of aquatic toxicity. Quant. Struct. Act. Relat. 14: 1–7.

    Google Scholar 

  • Degner P, Nendza M & Klein W (1991) Predictive QSAR models for estimating biodegradation of aromatic compounds. Sci. Total Environ. 109: 253–259

    Google Scholar 

  • Eastcott L, Shiu WY & Mackay D (1988) Environmentally relevant physical-chemical properties of hydrocarbons: a review of data and development of simple correlations. Oil & Chemical Pollution 4: 191–216

    Google Scholar 

  • Eriksson L, Johansson E & Wold S (1997) Quantitative structureactivity relationship model validation. In: Chen F & Schüürman G (Eds) Quantitative Structure-Activity Relationships in Environmental Sciences (pp 381–397). SETAC, Pensacola Hansch C, Leo A & Hoekman D (1995) Exploring QSAR: Hydrophobic, Electronic, and Steric Constants. ACS, Washington DC

  • Hermens, JLM (1995) Prediction of environmental toxicity based on structure-activity relationships using mechanistic information. Sci. Total Environ. 171: 235–242.

    Google Scholar 

  • Ikariyama Y, Nishiguchi S, Koyama T, Kobatake E & Aisawa M (1997) Fiber-optic-based biomonitoring of benzene derivatives by recombinant E. coli bearing luciferase gene-fused TOLplasmid immobilized on the fiber-optic end. Anal. Chem. 69: 2600–2605

    Google Scholar 

  • King JMH, DiGrazia PM, Applegate B, Burlage R, Sanseverino J, Dunbar P, Larimer, F & Sayler GS (1990) Rapid, sensitive bioluminescence reporter technology for naphthalene exposure and biodegradation. Science 249: 778–781

    Google Scholar 

  • Kragelund L, Christoffersen B, Nybroe O & de Bruijn FJ (1995) Isolation of lux reporter gene fusions in Pseudomonas fluorescens DF57 inducible by nitrogen or phosphorus starvation. FEMS Microbiol. Ecol. 17: 95–106

    Google Scholar 

  • Layton AC, Gregory B, Schultz TW & Sayler GS (1999) Validation of genetically engineered bioluminescent surfactant resistant bacteria as toxicity assessment tools. Ecotoxicol. Environ. Safety 43: 222–228

    Google Scholar 

  • Layton AC, Muccini M, Ghosh MM & Sayler GS (1998) Construction of a bioluminescent reporter strain to detect polychlorinated biphenyls. Appl. Environ. Microbiol. 64: 5023–5026

    Google Scholar 

  • Lipnick RL (1991) Outliers: their origin and use in the classification of molecular mechanisms of toxicity. Sci. Total Environ. 109/110: 131–153

    Google Scholar 

  • Lynam MM, Kuty M, Damborsky J, Koca J & Adriaens P (1998) Molecular orbital calculations to describe microbial reductive dechlorination of polychlorinated dioxins. Environ. Toxicol. Chem. 17: 988–997

    Google Scholar 

  • Marqués S & Ramos JL (1993) Transcriptional control of the Pseudomonas putida TOL plasmid catabolic pathways. Molecular Microbiol. 9: 923–929

    Google Scholar 

  • Meighen EA (1988) Enzymes and genes from the lux operons of bioluminescent bacteria. Ann. Rev. Microbiol. 42: 151–176

    Google Scholar 

  • Okey RW & Stensel HD (1996) A QSAR-based biodegradability model: a QSBR. Wat. Res. 30: 2206–2214

    Google Scholar 

  • Prest AG, Winson MK, Hammond JRM & Stewart GSAB (1997) Construction and application of a lux-based nitrate biosensor. Lett. Appl. Microbiol. 24: 355–360

    Google Scholar 

  • Selifonova O, Burlage R & Barkay T (1993) Bioluminescent sensors for detection of bioavailable Hg(II) in the environment. Appl. Environ. Microbiol. 59: 3083–3090

    Google Scholar 

  • Selifonova O & Eaton RW (1996) Use of an ipb-lux fusion to study regulation of the isopropylbenzene catabolism operon of Pseudomonas putida RE204 and to detect hydrophobic pollutants in the environment. Appl. Environ. Microbiol. 62: 778–783

    Google Scholar 

  • Sticher P, Jaspers MCM, Stemmler K, Harms H, Zehnder AJB & Van der Meer JR (1997) Development and characterization of a whole-cell bioluminescent sensor for bioavailable middle-chain alkanes in contaminated groundwater samples. Appl. Environ. Microbiol. 63: 4053–4060

    Google Scholar 

  • Tescione L & Belfort G (1993) Construction and evaluation of a metal-ion biosensor. Biotechnol. Bioeng. 42: 945–952

    Google Scholar 

  • van Beilen JB, Wubbolts MG & Witholt B (1994) Genetics of alkane oxidation by Pseudomonas oleovorans. Biodegradation 5: 161–174

    Google Scholar 

  • Willardson BM, Wilkins JF, Rand TA, Schupp JM, Hill KK, Keim P & Jackson PJ (1998) Development and testing of a bacterial biosensor for toluene-based environmental contaminants. Appl. Environ. Microbiol. 64: 1006–1012

    Google Scholar 

  • Williams PA & Sayers JR (1994) The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas. Biodegradation 5: 195–217

    Google Scholar 

  • Zylstra GJ & Gibson DT (1991) Aromatic hydrocarbon degradation: a molecular approach. Genetic Engineering 13: 183–203

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Plant and Soil Science, University of Aberdeen, Aberdeen, AB24 3UU, UK

    Jacob G. Bundy & Graeme I. Paton

  2. School of Pharmacy, Robert Gordon University, Schoolhill, Aberdeen, AB10 1FE, UK

    David G. Durham

  3. Soil Science Group, Macaulay Land Use Research Institute, Craigiebuckler, Aberdeen, AB15 8QH, UK

    Colin D. Campbell

Authors
  1. Jacob G. Bundy
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. David G. Durham
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Graeme I. Paton
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Colin D. Campbell
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Bundy, J.G., Durham, D.G., Paton, G.I. et al. Investigating the specificity of regulators of degradation of hydrocarbons and hydrocarbon-based compounds using structure-activity relationships. Biodegradation 11, 37–47 (2000). https://doi.org/10.1023/A:1026589401824

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1026589401824

Search

Navigation