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Solvent Tolerance in Bacteria: Fulfilling the Promise of the Biotech Era?

Kusumawardhani H, Hosseini R, de Winde JH.

Trends Biotechnol. 2018 Oct;36(10):1025-1039. doi: 10.1016/j.tibtech.2018.04.007. Epub 2018 May 16. Review.


Regulation of solvent tolerance in Pseudomonas putida S12 mediated by mobile elements.

Hosseini R, Kuepper J, Koebbing S, Blank LM, Wierckx N, de Winde JH.

Microb Biotechnol. 2017 Nov;10(6):1558-1568. doi: 10.1111/1751-7915.12495. Epub 2017 Apr 11.


Dynamic Response of Pseudomonas putida S12 to Sudden Addition of Toluene and the Potential Role of the Solvent Tolerance Gene trgI.

Volkers RJ, Snoek LB, Ruijssenaars HJ, de Winde JH.

PLoS One. 2015 Jul 16;10(7):e0132416. doi: 10.1371/journal.pone.0132416. eCollection 2015.


Complete genome sequence of solvent-tolerant Pseudomonas putida S12 including megaplasmid pTTS12.

Kuepper J, Ruijssenaars HJ, Blank LM, de Winde JH, Wierckx N.

J Biotechnol. 2015 Apr 20;200:17-8. doi: 10.1016/j.jbiotec.2015.02.027. Epub 2015 Mar 3.


The wicked problem of socially responsible innovation.

Flipse SM, De Winde JH, Osseweijer P, van der Sanden MC.

EMBO Rep. 2014 May;15(5):464. doi: 10.1002/embr.201438757. No abstract available.


The DNA of socially responsible innovation: Social and natural scientists need to establish mutual understanding and a common language to efficiently work together.

Flipse SM, van der Sanden MC, Radstake M, De Winde JH, Osseweijer P.

EMBO Rep. 2014 Feb;15(2):134-7. doi: 10.1002/embr.201337949. Epub 2014 Jan 17. No abstract available.


Crude glycerol as feedstock for the sustainable production of p-hydroxybenzoate by Pseudomonas putida S12.

Verhoef S, Gao N, Ruijssenaars HJ, de Winde JH.

N Biotechnol. 2014 Jan 25;31(1):114-9. doi: 10.1016/j.nbt.2013.08.006. Epub 2013 Aug 30.


Identification of a quinone dehydrogenase from a Bacillus sp. involved in the decolourization of the lignin-model dye, Azure B.

Bandounas L, Pinkse M, de Winde JH, Ruijssenaars HJ.

N Biotechnol. 2013 Jan 25;30(2):196-204. doi: 10.1016/j.nbt.2012.04.003. Epub 2012 Apr 27.


Metabolic and regulatory rearrangements underlying efficient D-xylose utilization in engineered Pseudomonas putida S12.

Meijnen JP, de Winde JH, Ruijssenaars HJ.

J Biol Chem. 2012 Apr 27;287(18):14606-14. doi: 10.1074/jbc.M111.337501. Epub 2012 Mar 13.


Cellular responses of Saccharomyces cerevisiae at near-zero growth rates: transcriptome analysis of anaerobic retentostat cultures.

Boender LG, van Maris AJ, de Hulster EA, Almering MJ, van der Klei IJ, Veenhuis M, de Winde JH, Pronk JT, Daran-Lapujade P.

FEMS Yeast Res. 2011 Dec;11(8):603-20. doi: 10.1111/j.1567-1364.2011.00750.x. Epub 2011 Sep 26.


Microbial degradation of furanic compounds: biochemistry, genetics, and impact.

Wierckx N, Koopman F, Ruijssenaars HJ, de Winde JH.

Appl Microbiol Biotechnol. 2011 Dec;92(6):1095-105. doi: 10.1007/s00253-011-3632-5. Epub 2011 Oct 28. Review.


Isolation and characterization of novel bacterial strains exhibiting ligninolytic potential.

Bandounas L, Wierckx NJ, de Winde JH, Ruijssenaars HJ.

BMC Biotechnol. 2011 Oct 13;11:94. doi: 10.1186/1472-6750-11-94.


Extreme calorie restriction and energy source starvation in Saccharomyces cerevisiae represent distinct physiological states.

Boender LG, Almering MJ, Dijk M, van Maris AJ, de Winde JH, Pronk JT, Daran-Lapujade P.

Biochim Biophys Acta. 2011 Dec;1813(12):2133-44. doi: 10.1016/j.bbamcr.2011.07.008. Epub 2011 Jul 22.


Redundancy in putrescine catabolism in solvent tolerant Pseudomonas putida S12.

Bandounas L, Ballerstedt H, de Winde JH, Ruijssenaars HJ.

J Biotechnol. 2011 Jun 10;154(1):1-10. doi: 10.1016/j.jbiotec.2011.04.005. Epub 2011 Apr 22.


Improved p-hydroxybenzoate production by engineered Pseudomonas putida S12 by using a mixed-substrate feeding strategy.

Meijnen JP, Verhoef S, Briedjlal AA, de Winde JH, Ruijssenaars HJ.

Appl Microbiol Biotechnol. 2011 May;90(3):885-93. doi: 10.1007/s00253-011-3089-6. Epub 2011 Feb 2.


Isolation and characterization of Cupriavidus basilensis HMF14 for biological removal of inhibitors from lignocellulosic hydrolysate.

Wierckx N, Koopman F, Bandounas L, de Winde JH, Ruijssenaars HJ.

Microb Biotechnol. 2010 May;3(3):336-43. doi: 10.1111/j.1751-7915.2009.00158.x. Epub 2009 Dec 15.


Isolation and genetic characterization of an improved benzene-tolerant mutant of Pseudomonas putida S12.

Volkers RJ, Ballerstedt H, De Winde JH, Ruijssenaars HJ.

Environ Microbiol Rep. 2010 Jun;2(3):456-60. doi: 10.1111/j.1758-2229.2010.00172.x.


Comparative transcriptomics and proteomics of p-hydroxybenzoate producing Pseudomonas putida S12: novel responses and implications for strain improvement.

Verhoef S, Ballerstedt H, Volkers RJ, de Winde JH, Ruijssenaars HJ.

Appl Microbiol Biotechnol. 2010 Jun;87(2):679-90. doi: 10.1007/s00253-010-2626-z. Epub 2010 May 7.


Efficient whole-cell biotransformation of 5-(hydroxymethyl)furfural into FDCA, 2,5-furandicarboxylic acid.

Koopman F, Wierckx N, de Winde JH, Ruijssenaars HJ.

Bioresour Technol. 2010 Aug;101(16):6291-6. doi: 10.1016/j.biortech.2010.03.050. Epub 2010 Apr 3.


Identification and characterization of the furfural and 5-(hydroxymethyl)furfural degradation pathways of Cupriavidus basilensis HMF14.

Koopman F, Wierckx N, de Winde JH, Ruijssenaars HJ.

Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):4919-24. doi: 10.1073/pnas.0913039107. Epub 2010 Mar 1.


Measuring enzyme activities under standardized in vivo-like conditions for systems biology.

van Eunen K, Bouwman J, Daran-Lapujade P, Postmus J, Canelas AB, Mensonides FI, Orij R, Tuzun I, van den Brink J, Smits GJ, van Gulik WM, Brul S, Heijnen JJ, de Winde JH, de Mattos MJ, Kettner C, Nielsen J, Westerhoff HV, Bakker BM.

FEBS J. 2010 Feb;277(3):749-60. doi: 10.1111/j.1742-4658.2009.07524.x. Epub 2010 Jan 7.


Metabolic flux analysis of a phenol producing mutant of Pseudomonas putida S12: verification and complementation of hypotheses derived from transcriptomics.

Wierckx N, Ruijssenaars HJ, de Winde JH, Schmid A, Blank LM.

J Biotechnol. 2009 Aug 20;143(2):124-9. doi: 10.1016/j.jbiotec.2009.06.023. Epub 2009 Jun 26.


Peroxicretion: a novel secretion pathway in the eukaryotic cell.

Sagt CM, ten Haaft PJ, Minneboo IM, Hartog MP, Damveld RA, van der Laan JM, Akeroyd M, Wenzel TJ, Luesken FA, Veenhuis M, van der Klei I, de Winde JH.

BMC Biotechnol. 2009 May 20;9:48. doi: 10.1186/1472-6750-9-48.


Energetic limits to metabolic flexibility: responses of Saccharomyces cerevisiae to glucose-galactose transitions.

van den Brink J, Akeroyd M, van der Hoeven R, Pronk JT, de Winde JH, Daran-Lapujade P.

Microbiology. 2009 Apr;155(Pt 4):1340-50. doi: 10.1099/mic.0.025775-0.


C(1) compounds as auxiliary substrate for engineered Pseudomonas putida S12.

Koopman FW, de Winde JH, Ruijssenaars HJ.

Appl Microbiol Biotechnol. 2009 Jun;83(4):705-13. doi: 10.1007/s00253-009-1922-y. Epub 2009 Mar 12.


Establishment of oxidative D-xylose metabolism in Pseudomonas putida S12.

Meijnen JP, de Winde JH, Ruijssenaars HJ.

Appl Environ Microbiol. 2009 May;75(9):2784-91. doi: 10.1128/AEM.02713-08. Epub 2009 Mar 6.


Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: a quantitative analysis of a compendium of chemostat-based transcriptome data.

Knijnenburg TA, Daran JM, van den Broek MA, Daran-Lapujade PA, de Winde JH, Pronk JT, Reinders MJ, Wessels LF.

BMC Genomics. 2009 Jan 27;10:53. doi: 10.1186/1471-2164-10-53.


TrgI, toluene repressed gene I, a novel gene involved in toluene-tolerance in Pseudomonas putida S12.

Volkers RJ, Ballerstedt H, Ruijssenaars H, de Bont JA, de Winde JH, Wery J.

Extremophiles. 2009 Mar;13(2):283-97. doi: 10.1007/s00792-008-0216-0. Epub 2008 Dec 17.


Bioproduction of p-hydroxystyrene from glucose by the solvent-tolerant bacterium Pseudomonas putida S12 in a two-phase water-decanol fermentation.

Verhoef S, Wierckx N, Westerhof RG, de Winde JH, Ruijssenaars HJ.

Appl Environ Microbiol. 2009 Feb;75(4):931-6. doi: 10.1128/AEM.02186-08. Epub 2008 Dec 5.


Chemostat-based micro-array analysis in baker's yeast.

Daran-Lapujade P, Daran JM, van Maris AJ, de Winde JH, Pronk JT.

Adv Microb Physiol. 2009;54:257-311. doi: 10.1016/S0065-2911(08)00004-0. Review.


Dynamics of glycolytic regulation during adaptation of Saccharomyces cerevisiae to fermentative metabolism.

van den Brink J, Canelas AB, van Gulik WM, Pronk JT, Heijnen JJ, de Winde JH, Daran-Lapujade P.

Appl Environ Microbiol. 2008 Sep;74(18):5710-23. doi: 10.1128/AEM.01121-08. Epub 2008 Jul 18.


Engineering Pseudomonas putida S12 for efficient utilization of D-xylose and L-arabinose.

Meijnen JP, de Winde JH, Ruijssenaars HJ.

Appl Environ Microbiol. 2008 Aug;74(16):5031-7. doi: 10.1128/AEM.00924-08. Epub 2008 Jun 27.


Saccharomyces cerevisiae SFP1: at the crossroads of central metabolism and ribosome biogenesis.

Cipollina C, van den Brink J, Daran-Lapujade P, Pronk JT, Porro D, de Winde JH.

Microbiology. 2008 Jun;154(Pt 6):1686-99. doi: 10.1099/mic.0.2008/017392-0.


New insights into the Saccharomyces cerevisiae fermentation switch: dynamic transcriptional response to anaerobicity and glucose-excess.

van den Brink J, Daran-Lapujade P, Pronk JT, de Winde JH.

BMC Genomics. 2008 Feb 27;9:100. doi: 10.1186/1471-2164-9-100.


Revisiting the role of yeast Sfp1 in ribosome biogenesis and cell size control: a chemostat study.

Cipollina C, van den Brink J, Daran-Lapujade P, Pronk JT, Vai M, de Winde JH.

Microbiology. 2008 Jan;154(Pt 1):337-46. doi: 10.1099/mic.0.2007/011767-0.


Transcriptome analysis of a phenol-producing Pseudomonas putida S12 construct: genetic and physiological basis for improved production.

Wierckx NJ, Ballerstedt H, de Bont JA, de Winde JH, Ruijssenaars HJ, Wery J.

J Bacteriol. 2008 Apr;190(8):2822-30. Epub 2007 Nov 9.


The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels.

Daran-Lapujade P, Rossell S, van Gulik WM, Luttik MA, de Groot MJ, Slijper M, Heck AJ, Daran JM, de Winde JH, Westerhoff HV, Pronk JT, Bakker BM.

Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15753-8. Epub 2007 Sep 26.


Transcriptional responses of Saccharomyces cerevisiae to preferred and nonpreferred nitrogen sources in glucose-limited chemostat cultures.

Boer VM, Tai SL, Vuralhan Z, Arifin Y, Walsh MC, Piper MD, de Winde JH, Pronk JT, Daran JM.

FEMS Yeast Res. 2007 Jun;7(4):604-20. Epub 2007 Apr 10.


Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88.

Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JA, van den Berg M, Breestraat S, Caddick MX, Contreras R, Cornell M, Coutinho PM, Danchin EG, Debets AJ, Dekker P, van Dijck PW, van Dijk A, Dijkhuizen L, Driessen AJ, d'Enfert C, Geysens S, Goosen C, Groot GS, de Groot PW, Guillemette T, Henrissat B, Herweijer M, van den Hombergh JP, van den Hondel CA, van der Heijden RT, van der Kaaij RM, Klis FM, Kools HJ, Kubicek CP, van Kuyk PA, Lauber J, Lu X, van der Maarel MJ, Meulenberg R, Menke H, Mortimer MA, Nielsen J, Oliver SG, Olsthoorn M, Pal K, van Peij NN, Ram AF, Rinas U, Roubos JA, Sagt CM, Schmoll M, Sun J, Ussery D, Varga J, Vervecken W, van de Vondervoort PJ, Wedler H, Wösten HA, Zeng AP, van Ooyen AJ, Visser J, Stam H.

Nat Biotechnol. 2007 Feb;25(2):221-31. Epub 2007 Jan 28.


Exploiting combinatorial cultivation conditions to infer transcriptional regulation.

Knijnenburg TA, de Winde JH, Daran JM, Daran-Lapujade P, Pronk JT, Reinders MJ, Wessels LF.

BMC Genomics. 2007 Jan 22;8:25.


Physiological characterization and fed-batch production of an extracellular maltase of Schizosaccharomyces pombe CBS 356.

Jansen ML, Krook DJ, De Graaf K, van Dijken JP, Pronk JT, de Winde JH.

FEMS Yeast Res. 2006 Sep;6(6):888-901.


Prolonged selection in aerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae causes a partial loss of glycolytic capacity.

Jansen ML, Diderich JA, Mashego M, Hassane A, de Winde JH, Daran-Lapujade P, Pronk JT.

Microbiology. 2005 May;151(Pt 5):1657-69.


Two-dimensional transcriptome analysis in chemostat cultures. Combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae.

Tai SL, Boer VM, Daran-Lapujade P, Walsh MC, de Winde JH, Daran JM, Pronk JT.

J Biol Chem. 2005 Jan 7;280(1):437-47. Epub 2004 Oct 20.


Prolonged maltose-limited cultivation of Saccharomyces cerevisiae selects for cells with improved maltose affinity and hypersensitivity.

Jansen ML, Daran-Lapujade P, de Winde JH, Piper MD, Pronk JT.

Appl Environ Microbiol. 2004 Apr;70(4):1956-63.


Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study.

Daran-Lapujade P, Jansen ML, Daran JM, van Gulik W, de Winde JH, Pronk JT.

J Biol Chem. 2004 Mar 5;279(10):9125-38. Epub 2003 Nov 20.


The role of hexose transport and phosphorylation in cAMP signalling in the yeast Saccharomyces cerevisiae.

Rolland F, Wanke V, Cauwenberg L, Ma P, Boles E, Vanoni M, de Winde JH, Thevelein JM, Winderickx J.

FEMS Yeast Res. 2001 Apr;1(1):33-45.

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