Skip to main content
SpringerLink
Log in

Experimental Evolution of Novel Regulatory Activities in Response to Hydrocarbons and Related Chemicals

  • Reference work entry
  • First Online:
Aerobic Utilization of Hydrocarbons, Oils, and Lipids

Part of the book series: Handbook of Hydrocarbon and Lipid Microbiology ((HHLM))

  • 1385 Accesses

Abstract

Bacterial transcriptional regulatory proteins that control catabolism of hydrocarbons and related chemicals have evolved (or are actively evolving) toward specifically detecting compounds that signal the presence of growth substrates. Laboratory evolution of the chemical-binding and response properties of sensory regulators has been achieved by a number of different techniques to generate novel derivatives with desired properties. Such manipulated and selected regulatory proteins are increasingly used in artificial genetic circuitry for improved biodegradation systems, biosensor construction, and in assembling regulatory cascades for synthetic biology within a wide range of biotechnological applications.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 239.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 279.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Beggah S, Vogne C, Zenaro E, van de Meer JR (2008) Mutant HbpR transcription activator isolation for 2-chlorobiphenyl via green flourescent protein-based flow cytometry and cell sorting. Microb Biotechnol 1:68–78

    CAS  PubMed  Google Scholar 

  • Cases I, de Lorenzo V (2005) Promoters in the environment: transcriptional regulation in its natural context. Nat Rev Microbiol 3:105–118

    Article  CAS  Google Scholar 

  • Cebolla A, Sousa C, de Lorenzo V (1997) Effector specificity mutants of the transcriptional activator NahR of naphthalene degrading Pseudomonas define protein sites involved in binding of aromatic inducers. J Biol Chem 272:3986–3992

    Article  CAS  Google Scholar 

  • Cebolla A, Sousa C, de Lorenzo V (2001) Rational design of a bacterial transcriptional cascade for amplifying gene expression capacity. Nucleic Acids Res 29:759–766

    Article  CAS  Google Scholar 

  • Collier DN, Spence C, Cox MJ, Phibbs PV (2001) Isolation and phenotypic characterization of Pseudomonas aeruginosa pseudorevertants containing suppressors of the catabolite repression control-defective crc-10 allele. FEMS Microbiol Lett 196:87–92

    Article  CAS  Google Scholar 

  • de Las HA, de Carreno CA, de Lorenzo V (2008) Stable implantation of orthogonal sensor circuits in Gram-negative bacteria for environmental release. Environ Microbiol 10:3305–3316

    Article  Google Scholar 

  • Delgado A, Ramos JL (1994) Genetic evidence for activation of the positive transcriptional regulator Xy1R, a member of the NtrC family of regulators, by effector binding. J Biol Chem 269:8059–8062

    CAS  PubMed  Google Scholar 

  • Devesse L, Smirnova I, Lonneborg R, Kapp U, Brzezinski P, Leonard GA, Dian C (2011) Crystal structures of DntR inducer binding domains in complex with salicylate offer insights into the activation of LysR-type transcriptional regulators. Mol Microbiol 81:354–367

    Article  CAS  Google Scholar 

  • Dominguez-Cuevas P, Marin P, Busby S, Ramos JL, Marques S (2008) Roles of effectors in XylS-dependent transcription activation: intramolecular domain derepression and DNA binding. J Bacteriol 190:3118–3128

    Article  CAS  Google Scholar 

  • Galvao TC, de Lorenzo V (2006) Transcriptional regulators a la carte: engineering new effector specificities in bacterial regulatory proteins. Curr Opin Biotechnol 17:34–42

    Article  CAS  Google Scholar 

  • Galvao TC, Mencia M, de Lorenzo V (2007) Emergence of novel functions in transcriptional regulators by regression to stem protein types. Mol Microbiol 65:907–919

    Article  CAS  Google Scholar 

  • Garmendia J, Devos D, Valencia A, de Lorenzo V (2001) A la carte transcriptional regulators: unlocking responses of the prokaryotic enhancer-binding protein XylR to non-natural effectors. Mol Microbiol 42:47–59

    Article  CAS  Google Scholar 

  • Gupta S, Saxena M, Saini N, Mahmooduzzafar, Kumar R, Kumar A (2012) An effective strategy for a whole-cell biosensor based on putative effector interaction site of the regulatory DmpR protein. PLOS ONE 7:e43527

    Article  CAS  Google Scholar 

  • Kwon HJ, Bennik MH, Demple B, Ellenberger T (2000) Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA. Nat Struct Biol 7:424–430

    Article  CAS  Google Scholar 

  • Lonneborg R, Smirnova I, Dian C, Leonard GA, Brzezinski P (2007) In vivo and in vitro investigation of transcriptional regulation by DntR. J Mol Biol 372:571–582

    Article  Google Scholar 

  • Lonneborg R, Varga E, Brzezinski P (2012) Directed evolution of the transcriptional regulator DntR: isolation of mutants with improved DNT-response. PLoS One 7:e29994

    Article  Google Scholar 

  • Looger LL, Dwyer MA, Smith JJ, Hellinga HW (2003) Computational design of receptor and sensor proteins with novel functions. Nature 423:185–190

    Article  CAS  Google Scholar 

  • Maddocks SE, Oyston PC (2008) Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins. Microbiology 154:3609–3623

    Article  CAS  Google Scholar 

  • Mahr R, Frunzke J (2016) Transcription factor-based biosensors in biotechnology: current state and future prospects. Appl Microbiol Biotechnol 100:79–90

    Article  CAS  Google Scholar 

  • Michan C, Zhou L, Gallegos MT, Timmis KN, Ramos JL (1992) Identification of critical amino-terminal regions of XylS. The positive regulator encoded by the TOL plasmid. J Biol Chem 267:22897–22901

    CAS  PubMed  Google Scholar 

  • Mohn WW, Garmendia J, Galvao TC, de Lorenzo V (2006) Surveying biotransformations with a la carte genetic traps: translating dehydrochlorination of lindane (gamma-hexachlorocyclohexane) into lacZ-based phenotypes. Environ Microbiol 8:546–555

    Article  CAS  Google Scholar 

  • Ng LC, O’Neill E, Shingler V (1996) Genetic evidence for interdomain regulation of the phenol-responsive final σ 54-dependent activator DmpR. J Biol Chem 271:17281–17286

    Article  CAS  Google Scholar 

  • O’Neill E, Sze CC, Shingler V (1999) Novel effector control through modulation of a preexisting binding site of the aromatic-responsive σ 54-dependent regulator DmpR. J Biol Chem 274:32425–32432

    Article  Google Scholar 

  • O’Neill E, Wikstrom P, Shingler V (2001) An active role for a structured B-linker in effector control of the σ 54-dependent regulator DmpR. EMBO J 20:819–827

    Article  Google Scholar 

  • Park HH, Lee HY, Lim WK, Shin HJ (2005) NahR: effects of replacements at Asn 169 and Arg 248 on promoter binding and inducer recognition. Arch Biochem Biophys 434:67–74

    Article  CAS  Google Scholar 

  • Patil VV, Park KH, Lee SG, Woo E (2016) Structural analysis of the phenol-responsive sensory domain of the transcription activator PoxR. Structure 24:624–630

    Article  CAS  Google Scholar 

  • Pavel H, Forsman M, Shingler V (1994) An aromatic effector specificity mutant of the transcriptional regulator DmpR overcomes the growth constraints of Pseudomonas sp. strain CF600 on para-substituted methylphenols. J Bacteriol 176:7550–7557

    Article  CAS  Google Scholar 

  • Ramos JL, Stolz A, Reineke W, Timmis KN (1986) Altered effector specificities in regulators of gene expression: TOL plasmid xylS mutants and their use to engineer expansion of the range of aromatics degraded by bacteria. Proc Natl Acad Sci USA 83:8467–8471

    Article  CAS  Google Scholar 

  • Reimer A, Yagur-Kroll S, Belkin S, Roy S, van der Meer JR (2014) Escherichia coli ribose binding protein based bioreporters revisited. Sci Rep 4:5626

    Article  CAS  Google Scholar 

  • Rhee S, Martin RG, Rosner JL, Davies DR (1998) A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator. Proc Natl Acad Sci USA 95:10413–10418

    Article  CAS  Google Scholar 

  • Royo JL, Becker PD, Camacho EM, Cebolla A, Link C, Santero E, Guzman CA (2007) In vivo gene regulation in Salmonella spp. by a salicylate-dependent control circuit. Nat Methods 4:937–942

    Article  CAS  Google Scholar 

  • Sarand I, Skarfstad E, Forsman M, Romantschuk M, Shingler V (2001) Role of the DmpR-mediated regulatory circuit in bacterial biodegradation properties in methylphenol-amended soils. Appl Environ Microbiol 67:162–171

    Article  CAS  Google Scholar 

  • Schleif R (2003) AraC protein: a love-hate relationship. BioEssays 25:274–282

    Article  CAS  Google Scholar 

  • Shingler V (2003) Integrated regulation in response to aromatic compounds: from signal sensing to attractive behaviour. Environ Microbiol 5:1226–1241

    Article  CAS  Google Scholar 

  • Shingler V (2011) Signal sensory systems that impact σ54-dependent transcription. FEMS Microbiol Rev 35:425–440

    Article  CAS  Google Scholar 

  • Silva-Rocha R, de Lorenzo V (2008) Mining logic gates in prokaryotic transcriptional regulation networks. FEBS Lett 582:1237–1244

    Article  CAS  Google Scholar 

  • Skärfstad E, O’Neill E, Garmendia J, Shingler V (2000) Identification of an effector specificity subregion within the aromatic-responsive regulators DmpR and XylR by DNA shuffling. J Bacteriol 182:3008–3016

    Article  Google Scholar 

  • Stagno JR, Liu Y, Bhandari YR, Conrad CE, Panja S, Swain M, Fan L, Nelson G, Li C, Wendel DR, White TA, Coe JD, Wiedorn MO, Knoska J, Oberthuer D, Tuckey RA, Yu P, Dyba M, Tarasov SG, Weierstall U et al (2016) Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography. Nature. doi:10.1038/nature20599

    Article  PubMed  PubMed Central  Google Scholar 

  • Tropel D, van der Meer JR (2004) Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Microbiol Mol Biol Rev 68:474–500

    Article  CAS  Google Scholar 

  • Uchiyama T, Abe T, Ikemura T, Watanabe K (2005) Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat Biotechnol 23:88–93

    Article  CAS  Google Scholar 

  • van der Meer JR, Belkin S (2010) Where microbiology meets microengineering: design and applications of reporter bacteria. Nat Rev Microbiol 8:511–522

    Article  Google Scholar 

  • van Sint FS, Beilen JB, van Witholt B (2006) Selection of biocatalysts for chemical synthesis. Proc Natl Acad Sci USA 103:1693–1698

    Article  Google Scholar 

  • Wikström P, O’Neill E, Ng LC, Shingler V (2001) The regulatory N-terminal region of the aromatic-responsive transcriptional activator DmpR constrains nucleotide-triggered multimerisation. J Mol Biol 314:971–984

    Article  Google Scholar 

  • Wise AA, Kuske CR (2000) Generation of novel bacterial regulatory proteins that detect priority pollutant phenols. Appl Environ Microbiol 66:163–169

    Article  CAS  Google Scholar 

  • Zhang N, Darbari VC, Glyde R, Zhang X, Buck M (2016) The bacterial enhancer-dependent RNA polymerase. Biochem J 473:3741–3753

    Article  CAS  Google Scholar 

Download references

Acknowledgments

Research in the Shingler laboratory is supported by the Swedish Research Council (VR-MH 2016-02047) and the JC Kempe and SM Kempe foundation (JCK-1523).

Author information

Authors and Affiliations

  1. Department of Molecular Biology, Umeå University, Umeå, Sweden

    V. Shingler

Authors
  1. V. Shingler
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to V. Shingler .

Editor information

Editors and Affiliations

  1. Centro Nacional de Biotecnología, CSIC, Madrid, Spain

    Fernando Rojo

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this entry

Check for updates. Verify currency and authenticity via CrossMark

Cite this entry

Shingler, V. (2019). Experimental Evolution of Novel Regulatory Activities in Response to Hydrocarbons and Related Chemicals. In: Rojo, F. (eds) Aerobic Utilization of Hydrocarbons, Oils, and Lipids. Handbook of Hydrocarbon and Lipid Microbiology . Springer, Cham. https://doi.org/10.1007/978-3-319-50418-6_34

Download citation

Publish with us

Policies and ethics

Search

Navigation