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Draft Genome Sequence of the Caffeine-Degrading Methylotroph Methylorubrum populi Pinkel.

Parales RE, Sharma G, Zhang X, Subuyuj GA, Langner JT, Wright ME, Ditty JL, Dawson SC.

Microbiol Resour Announc. 2019 Nov 21;8(47). pii: e01300-19. doi: 10.1128/MRA.01300-19.


Hybrid Two-Component Sensors for Identification of Bacterial Chemoreceptor Function.

Luu RA, Schomer RA, Brunton CN, Truong R, Ta AP, Tan WA, Parales JV, Wang YJ, Huo YW, Liu SJ, Ditty JL, Stewart V, Parales RE.

Appl Environ Microbiol. 2019 Oct 30;85(22). pii: e01626-19. doi: 10.1128/AEM.01626-19. Print 2019 Nov 15.


Chemotaxis of Pseudomonas putida F1 to Alcohols Is Mediated by the Carboxylic Acid Receptor McfP.

Zhang X, Hughes JG, Subuyuj GA, Ditty JL, Parales RE.

Appl Environ Microbiol. 2019 Oct 30;85(22). pii: e01625-19. doi: 10.1128/AEM.01625-19. Print 2019 Nov 15.


Phenotype-centric modeling for elucidation of biological design principles.

Valderrama-Gómez MA, Parales RE, Savageau MA.

J Theor Biol. 2018 Oct 14;455:281-292. doi: 10.1016/j.jtbi.2018.07.009. Epub 2018 Jul 20.


Chemotaxis to Atypical Chemoattractants by Soil Bacteria.

Parales RE, Ditty JL.

Methods Mol Biol. 2018;1729:255-280. doi: 10.1007/978-1-4939-7577-8_21.


Genome Sequence of Pseudomonas putida Strain ASAD, an Acetylsalicylic Acid-Degrading Bacterium.

Parales RE, Navara R, Gettys R, Huang JJ.

Genome Announc. 2017 Oct 12;5(41). pii: e01169-17. doi: 10.1128/genomeA.01169-17.


Pseudomonas putida F1 uses energy taxis to sense hydroxycinnamic acids.

Hughes JG, Zhang X, Parales JV, Ditty JL, Parales RE.

Microbiology. 2017 Oct;163(10):1490-1501. doi: 10.1099/mic.0.000533. Epub 2017 Sep 28.


Direct sensing and signal transduction during bacterial chemotaxis toward aromatic compounds in Comamonas testosteroni.

Huang Z, Ni B, Jiang CY, Wu YF, He YZ, Parales RE, Liu SJ.

Mol Microbiol. 2016 Jul;101(2):224-37. doi: 10.1111/mmi.13385. Epub 2016 May 2.


Substrate and Enzyme Specificity of the Kinetic Isotope Effects Associated with the Dioxygenation of Nitroaromatic Contaminants.

Pati SG, Kohler HP, Pabis A, Paneth P, Parales RE, Hofstetter TB.

Environ Sci Technol. 2016 Jul 5;50(13):6708-16. doi: 10.1021/acs.est.5b05084. Epub 2016 Mar 7.


Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment.

Timm CM, Campbell AG, Utturkar SM, Jun SR, Parales RE, Tan WA, Robeson MS, Lu TY, Jawdy S, Brown SD, Ussery DW, Schadt CW, Tuskan GA, Doktycz MJ, Weston DJ, Pelletier DA.

Front Microbiol. 2015 Oct 14;6:1118. doi: 10.3389/fmicb.2015.01118. eCollection 2015.


Bacterial chemotaxis to xenobiotic chemicals and naturally-occurring analogs.

Parales RE, Luu RA, Hughes JG, Ditty JL.

Curr Opin Biotechnol. 2015 Jun;33:318-26. doi: 10.1016/j.copbio.2015.03.017. Epub 2015 Apr 15. Review.


Integration of chemotaxis, transport and catabolism in Pseudomonas putida and identification of the aromatic acid chemoreceptor PcaY.

Luu RA, Kootstra JD, Nesteryuk V, Brunton CN, Parales JV, Ditty JL, Parales RE.

Mol Microbiol. 2015 Apr;96(1):134-47. doi: 10.1111/mmi.12929. Epub 2015 Feb 12.


David T. Gibson: from biodegradation to biocatalysis.

Harwood CS, Parales RE.

Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):16980-1. doi: 10.1073/pnas.1420371111. Epub 2014 Nov 24. No abstract available.


Selection for growth on 3-nitrotoluene by 2-nitrotoluene-utilizing Acidovorax sp. strain JS42 identifies nitroarene dioxygenases with altered specificities.

Mahan KM, Penrod JT, Ju KS, Al Kass N, Tan WA, Truong R, Parales JV, Parales RE.

Appl Environ Microbiol. 2015 Jan;81(1):309-19. doi: 10.1128/AEM.02772-14. Epub 2014 Oct 24.


Cytosine chemoreceptor McpC in Pseudomonas putida F1 also detects nicotinic acid.

Parales RE, Nesteryuk V, Hughes JG, Luu RA, Ditty JL.

Microbiology. 2014 Dec;160(Pt 12):2661-2669. doi: 10.1099/mic.0.081968-0. Epub 2014 Oct 7.


Isotope effects of enzymatic dioxygenation of nitrobenzene and 2-nitrotoluene by nitrobenzene dioxygenase.

Pati SG, Kohler HP, Bolotin J, Parales RE, Hofstetter TB.

Environ Sci Technol. 2014 Sep 16;48(18):10750-9. doi: 10.1021/es5028844. Epub 2014 Aug 26.


Pseudomonas chemotaxis.

Sampedro I, Parales RE, Krell T, Hill JE.

FEMS Microbiol Rev. 2015 Jan;39(1):17-46. doi: 10.1111/1574-6976.12081. Epub 2014 Dec 4. Review.


Oxidation of the cyclic ethers 1,4-dioxane and tetrahydrofuran by a monooxygenase in two Pseudonocardia species.

Sales CM, Grostern A, Parales JV, Parales RE, Alvarez-Cohen L.

Appl Environ Microbiol. 2013 Dec;79(24):7702-8. doi: 10.1128/AEM.02418-13. Epub 2013 Oct 4.


Pseudomonas putida F1 has multiple chemoreceptors with overlapping specificity for organic acids.

Parales RE, Luu RA, Chen GY, Liu X, Wu V, Lin P, Hughes JG, Nesteryuk V, Parales JV, Ditty JL.

Microbiology. 2013 Jun;159(Pt 6):1086-1096. doi: 10.1099/mic.0.065698-0. Epub 2013 Apr 25.


Integrating grant-funded research into the undergraduate biology curriculum using IMG-ACT.

Ditty JL, Williams KM, Keller MM, Chen GY, Liu X, Parales RE.

Biochem Mol Biol Educ. 2013 Jan-Feb;41(1):16-23. doi: 10.1002/bmb.20662.


Taxis of Pseudomonas putida F1 toward phenylacetic acid is mediated by the energy taxis receptor Aer2.

Luu RA, Schneider BJ, Ho CC, Nesteryuk V, Ngwesse SE, Liu X, Parales JV, Ditty JL, Parales RE.

Appl Environ Microbiol. 2013 Apr;79(7):2416-23. doi: 10.1128/AEM.03895-12. Epub 2013 Feb 1.


Three types of taxis used in the response of Acidovorax sp. strain JS42 to 2-nitrotoluene.

Rabinovitch-Deere CA, Parales RE.

Appl Environ Microbiol. 2012 Apr;78(7):2306-15. doi: 10.1128/AEM.07183-11. Epub 2012 Jan 27.


Role of IncP-1β plasmids pWDL7::rfp and pNB8c in chloroaniline catabolism as determined by genomic and functional analyses.

Król JE, Penrod JT, McCaslin H, Rogers LM, Yano H, Stancik AD, Dejonghe W, Brown CJ, Parales RE, Wuertz S, Top EM.

Appl Environ Microbiol. 2012 Feb;78(3):828-38. doi: 10.1128/AEM.07480-11. Epub 2011 Nov 18.


Evolution of a new bacterial pathway for 4-nitrotoluene degradation.

Ju KS, Parales RE.

Mol Microbiol. 2011 Oct;82(2):355-64. doi: 10.1111/j.1365-2958.2011.07817.x. Epub 2011 Sep 13.


Genome sequence of the 1,4-dioxane-degrading Pseudonocardia dioxanivorans strain CB1190.

Sales CM, Mahendra S, Grostern A, Parales RE, Goodwin LA, Woyke T, Nolan M, Lapidus A, Chertkov O, Ovchinnikova G, Sczyrba A, Alvarez-Cohen L.

J Bacteriol. 2011 Sep;193(17):4549-50. doi: 10.1128/JB.00415-11. Epub 2011 Jul 1.


Effects of phenolic monomers on growth of Acidothermus cellulolyticus.

Joh LD, Rezaei F, Barabote RD, Parales JV, Parales RE, Berry AM, Vandergheynst JS.

Biotechnol Prog. 2011 Jan-Feb;27(1):23-31. doi: 10.1002/btpr.525. Epub 2010 Dec 22.


Xyn10A, a thermostable endoxylanase from Acidothermus cellulolyticus 11B.

Barabote RD, Parales JV, Guo YY, Labavitch JM, Parales RE, Berry AM.

Appl Environ Microbiol. 2010 Nov;76(21):7363-6. doi: 10.1128/AEM.01326-10. Epub 2010 Sep 17.


The surprising Rut pathway: an unexpected way to derive nitrogen from pyrimidines.

Parales RE, Ingraham JL.

J Bacteriol. 2010 Aug;192(16):4086-8. doi: 10.1128/JB.00573-10. Epub 2010 Jun 18. No abstract available.


Nitroaromatic compounds, from synthesis to biodegradation.

Ju KS, Parales RE.

Microbiol Mol Biol Rev. 2010 Jun;74(2):250-72. doi: 10.1128/MMBR.00006-10. Review.


Identification of a chemoreceptor for tricarboxylic acid cycle intermediates: differential chemotactic response towards receptor ligands.

Lacal J, Alfonso C, Liu X, Parales RE, Morel B, Conejero-Lara F, Rivas G, Duque E, Ramos JL, Krell T.

J Biol Chem. 2010 Jul 23;285(30):23126-36. doi: 10.1074/jbc.M110.110403. Epub 2010 May 24.


Pseudomonas taeanensis sp. nov., isolated from a crude oil-contaminated seashore.

Lee DH, Moon SR, Park YH, Kim JH, Kim H, Parales RE, Kahng HY.

Int J Syst Evol Microbiol. 2010 Dec;60(Pt 12):2719-23. doi: 10.1099/ijs.0.018093-0. Epub 2010 Jan 8.


Reconstructing the evolutionary history of nitrotoluene detection in the transcriptional regulator NtdR.

Ju KS, Parales JV, Parales RE.

Mol Microbiol. 2009 Nov;74(4):826-43. doi: 10.1111/j.1365-2958.2009.06904.x. Epub 2009 Oct 22.


Bacterial chemotaxis to atrazine and related s-triazines.

Liu X, Parales RE.

Appl Environ Microbiol. 2009 Sep;75(17):5481-8. doi: 10.1128/AEM.01030-09. Epub 2009 Jul 6.


Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations.

Barabote RD, Xie G, Leu DH, Normand P, Necsulea A, Daubin V, Médigue C, Adney WS, Xu XC, Lapidus A, Parales RE, Detter C, Pujic P, Bruce D, Lavire C, Challacombe JF, Brettin TS, Berry AM.

Genome Res. 2009 Jun;19(6):1033-43. doi: 10.1101/gr.084848.108. Epub 2009 Mar 6.


Chemotaxis to pyrimidines and identification of a cytosine chemoreceptor in Pseudomonas putida.

Liu X, Wood PL, Parales JV, Parales RE.

J Bacteriol. 2009 May;191(9):2909-16. doi: 10.1128/JB.01708-08. Epub 2009 Feb 27.


Application of nitroarene dioxygenases in the design of novel strains that degrade chloronitrobenzenes.

Ju KS, Parales RE.

Microb Biotechnol. 2009 Mar;2(2):241-52. doi: 10.1111/j.1751-7915.2008.00083.x.


Diversity of microbial toluene degradation pathways.

Parales RE, Parales JV, Pelletier DA, Ditty JL.

Adv Appl Microbiol. 2008;64:1-73, 2 p following 264. doi: 10.1016/S0065-2164(08)00401-2. Review. No abstract available.


Metabolism-dependent taxis towards (methyl)phenols is coupled through the most abundant of three polar localized Aer-like proteins of Pseudomonas putida.

Sarand I, Osterberg S, Holmqvist S, Holmfeldt P, Skärfstad E, Parales RE, Shingler V.

Environ Microbiol. 2008 May;10(5):1320-34. doi: 10.1111/j.1462-2920.2007.01546.x. Epub 2008 Feb 12.


Pseudomonas 2007.

Goldberg JB, Hancock RE, Parales RE, Loper J, Cornelis P.

J Bacteriol. 2008 Apr;190(8):2649-62. doi: 10.1128/JB.01950-07. Epub 2007 Dec 28. No abstract available.


Chemotaxis of Escherichia coli to pyrimidines: a new role for the signal transducer tap.

Liu X, Parales RE.

J Bacteriol. 2008 Feb;190(3):972-9. Epub 2007 Dec 7.


Purification, characterization, and crystallization of the components of a biphenyl dioxygenase system from Sphingobium yanoikuyae B1.

Yu CL, Liu W, Ferraro DJ, Brown EN, Parales JV, Ramaswamy S, Zylstra GJ, Gibson DT, Parales RE.

J Ind Microbiol Biotechnol. 2007 Apr;34(4):311-24. Epub 2007 Jan 9.


Novel organization of catechol meta pathway genes in the nitrobenzene degrader Comamonas sp. JS765 and its evolutionary implication.

He Z, Parales RE, Spain JC, Johnson GR.

J Ind Microbiol Biotechnol. 2007 Feb;34(2):99-104. Epub 2006 Sep 1.


Control of substrate specificity by active-site residues in nitrobenzene dioxygenase.

Ju KS, Parales RE.

Appl Environ Microbiol. 2006 Mar;72(3):1817-24.


Active site residues controlling substrate specificity in 2-nitrotoluene dioxygenase from Acidovorax sp. strain JS42.

Lee KS, Parales JV, Friemann R, Parales RE.

J Ind Microbiol Biotechnol. 2005 Oct;32(10):465-73. Epub 2005 Oct 15.


Purification, characterization, and crystallization of the components of the nitrobenzene and 2-nitrotoluene dioxygenase enzyme systems.

Parales RE, Huang R, Yu CL, Parales JV, Lee FK, Lessner DJ, Ivkovic-Jensen MM, Liu W, Friemann R, Ramaswamy S, Gibson DT.

Appl Environ Microbiol. 2005 Jul;71(7):3806-14.


Laboratory evolution of catabolic enzymes and pathways.

Parales RE, Ditty JL.

Curr Opin Biotechnol. 2005 Jun;16(3):315-25. Review.


NO binding to naphthalene dioxygenase.

Karlsson A, Parales JV, Parales RE, Gibson DT, Eklund H, Ramaswamy S.

J Biol Inorg Chem. 2005 Aug;10(5):483-9. Epub 2005 Sep 23.


Structural insight into the dioxygenation of nitroarene compounds: the crystal structure of nitrobenzene dioxygenase.

Friemann R, Ivkovic-Jensen MM, Lessner DJ, Yu CL, Gibson DT, Parales RE, Eklund H, Ramaswamy S.

J Mol Biol. 2005 May 20;348(5):1139-51. Epub 2005 Apr 7.


Biocatalytic synthesis of polycatechols from toxic aromatic compounds.

Ward G, Parales RE, Dosoretz CG.

Environ Sci Technol. 2004 Sep 15;38(18):4753-7.


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