Escherichia [corrected] Coli Ribose Binding Protein Based Bioreporters Revisited

Overview

Journal Sci Rep

Specialty Science

Date 2014 Jul 10

PMID 25005019

Citations 7

Authors

Artur Reimer

Sharon Yagur-Kroll

Shimshon Belkin

Shantanu Roy

Jan Roelof van der Meer

Affiliations

Soon will be listed here.

Abstract

Bioreporter bacteria, i.e., strains engineered to respond to chemical exposure by production of reporter proteins, have attracted wide interest because of their potential to offer cheap and simple alternative analytics for specified compounds or conditions. Bioreporter construction has mostly exploited the natural variation of sensory proteins, but it has been proposed that computational design of new substrate binding properties could lead to completely novel detection specificities at very low affinities. Here we reconstruct a bioreporter system based on the native Escherichia coli ribose binding protein RbsB and one of its computationally designed variants, reported to be capable of binding 2,4,6-trinitrotoluene (TNT). Our results show in vivo reporter induction at 50 nM ribose, and a 125 nM affinity constant for in vitro ribose binding to RbsB. In contrast, the purified published TNT-binding variant did not bind TNT nor did TNT cause induction of the E. coli reporter system.

Citing Articles

Subcellular Localization Defects Characterize Ribose-Binding Mutant Proteins with New Ligand Properties in Escherichia coli.

Tavares D, van der Meer J Appl Environ Microbiol. 2021; 88(2):e0211721.

PMID: 34757821 PMC: 8788693. DOI: 10.1128/AEM.02117-21.

Ribose-Binding Protein Mutants With Improved Interaction Towards the Non-natural Ligand 1,3-Cyclohexanediol.

Tavares D, van der Meer J Front Bioeng Biotechnol. 2021; 9:705534.

PMID: 34368100 PMC: 8343135. DOI: 10.3389/fbioe.2021.705534.

Computational redesign of the Escherichia coli ribose-binding protein ligand binding pocket for 1,3-cyclohexanediol and cyclohexanol.

Tavares D, Reimer A, Roy S, Joublin A, Sentchilo V, van der Meer J Sci Rep. 2019; 9(1):16940.

PMID: 31729460 PMC: 6858440. DOI: 10.1038/s41598-019-53507-5.

Determination of Ligand Profiles for Solute Binding Proteins.

Fernandez M, Rico-Jimenez M, Ortega A, Daddaoua A, Garcia Garcia A, Martin-Mora D Int J Mol Sci. 2019; 20(20).

PMID: 31627455 PMC: 6829864. DOI: 10.3390/ijms20205156.

Probing chemotaxis activity in Escherichia coli using fluorescent protein fusions.

Roggo C, Carraro N, van der Meer J Sci Rep. 2019; 9(1):3845.

PMID: 30846802 PMC: 6405996. DOI: 10.1038/s41598-019-40655-x.

References

Chu B, Vogel H . A structural and functional analysis of type III periplasmic and substrate binding proteins: their role in bacterial siderophore and heme transport. Biol Chem. 2011; 392(1-2):39-52. DOI: 10.1515/BC.2011.012. View

Sticher P, Jaspers M, Stemmler K, Harms H, Zehnder A, van der Meer J . Development and characterization of a whole-cell bioluminescent sensor for bioavailable middle-chain alkanes in contaminated groundwater samples. Appl Environ Microbiol. 1997; 63(10):4053-60. PMC: 168716. DOI: 10.1128/aem.63.10.4053-4060.1997. View

Mustafi N, Grunberger A, Kohlheyer D, Bott M, Frunzke J . The development and application of a single-cell biosensor for the detection of l-methionine and branched-chain amino acids. Metab Eng. 2012; 14(4):449-57. DOI: 10.1016/j.ymben.2012.02.002. View

Srividhya K, Krishnaswamy S . A simulation model of Escherichia coli osmoregulatory switch using E-CELL system. BMC Microbiol. 2004; 4:44. PMC: 543474. DOI: 10.1186/1471-2180-4-44. View

Grimm S, Salahshour S, Nygren P . Monitored whole gene in vitro evolution of an anti-hRaf-1 affibody molecule towards increased binding affinity. N Biotechnol. 2011; 29(5):534-42. DOI: 10.1016/j.nbt.2011.10.008. View

Reed B, Blazeck J, Alper H . Evolution of an alkane-inducible biosensor for increased responsiveness to short-chain alkanes. J Biotechnol. 2012; 158(3):75-9. DOI: 10.1016/j.jbiotec.2012.01.028. View

Branco R, Cristovao A, Morais P . Highly sensitive, highly specific whole-cell bioreporters for the detection of chromate in environmental samples. PLoS One. 2013; 8(1):e54005. PMC: 3543429. DOI: 10.1371/journal.pone.0054005. View

Dwyer M, Looger L, Hellinga H . Computational design of a Zn2+ receptor that controls bacterial gene expression. Proc Natl Acad Sci U S A. 2003; 100(20):11255-60. PMC: 208744. DOI: 10.1073/pnas.2032284100. View

Schreier B, Stumpp C, Wiesner S, Hocker B . Computational design of ligand binding is not a solved problem. Proc Natl Acad Sci U S A. 2009; 106(44):18491-6. PMC: 2773959. DOI: 10.1073/pnas.0907950106. View

10.

Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S . A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods. 2006; 3(8):623-8. DOI: 10.1038/nmeth895. View

11.

Stocker J, Balluch D, Gsell M, Harms H, Feliciano J, Daunert S . Development of a set of simple bacterial biosensors for quantitative and rapid measurements of arsenite and arsenate in potable water. Environ Sci Technol. 2003; 37(20):4743-50. DOI: 10.1021/es034258b. View

12.

Studier F, Moffatt B . Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol. 1986; 189(1):113-30. DOI: 10.1016/0022-2836(86)90385-2. View

13.

Farhan Ul Haque M, Nadalig T, Bringel F, Schaller H, Vuilleumier S . Fluorescence-based bacterial bioreporter for specific detection of methyl halide emissions in the environment. Appl Environ Microbiol. 2013; 79(21):6561-7. PMC: 3811496. DOI: 10.1128/AEM.01738-13. View

14.

Binnie R, Zhang H, MOWBRAY S, Hermodson M . Functional mapping of the surface of Escherichia coli ribose-binding protein: mutations that affect chemotaxis and transport. Protein Sci. 1992; 1(12):1642-51. PMC: 2142133. DOI: 10.1002/pro.5560011212. View

15.

Munoz-Martin M, Mateo P, Leganes F, Fernandez-Pinas F . A battery of bioreporters of nitrogen bioavailability in aquatic ecosystems based on cyanobacteria. Sci Total Environ. 2013; 475:169-79. DOI: 10.1016/j.scitotenv.2013.07.015. View

16.

Beggah S, Vogne C, Zenaro E, van der Meer J . Mutant HbpR transcription activator isolation for 2-chlorobiphenyl via green fluorescent protein-based flow cytometry and cell sorting. Microb Biotechnol. 2011; 1(1):68-78. PMC: 3864433. DOI: 10.1111/j.1751-7915.2007.00008.x. View

17.

Azoitei M, Correia B, Ban Y, Carrico C, Kalyuzhniy O, Chen L . Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold. Science. 2011; 334(6054):373-6. DOI: 10.1126/science.1209368. View

18.

Galvao T, de Lorenzo V . Transcriptional regulators à la carte: engineering new effector specificities in bacterial regulatory proteins. Curr Opin Biotechnol. 2005; 17(1):34-42. DOI: 10.1016/j.copbio.2005.12.002. View

19.

Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M . Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol. 2006; 2:2006.0008. PMC: 1681482. DOI: 10.1038/msb4100050. View

20.

Belkin S . A panel of stress-responsive luminous bacteria for monitoring wastewater toxicity. Methods Mol Biol. 1998; 102:247-58. DOI: 10.1385/0-89603-520-4:247. View