TY - JOUR AU - Wiser, M. J. AU - Ribeck, N. AU - Lenski, R. E. PY - 2013 DA - 2013// TI - Long-term dynamics of adaptation in asexual populations JO - Science VL - 342 UR - https://doi.org/10.1126/science.1243357 DO - 10.1126/science.1243357 ID - Wiser2013 ER - TY - JOUR AU - Bachmann, H. AU - Starrenburg, M. J. C. AU - Molenaar, D. AU - Kleerebezem, M. AU - Hylckama Vlieg, J. E. T. PY - 2012 DA - 2012// TI - Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution JO - Genome Res VL - 22 UR - https://doi.org/10.1101/gr.121285.111 DO - 10.1101/gr.121285.111 ID - Bachmann2012 ER - TY - JOUR AU - Lázár, V. AU - Pal Singh, G. AU - Spohn, R. AU - Nagy, I. AU - Horváth, B. AU - Hrtyan, M. PY - 2013 DA - 2013// TI - Bacterial evolution of antibiotic hypersensitivity JO - Mol Syst Biol VL - 9 UR - https://doi.org/10.1038/msb.2013.57 DO - 10.1038/msb.2013.57 ID - Lázár2013 ER - TY - JOUR AU - Gresham, D. AU - Hong, J. PY - 2014 DA - 2014// TI - The functional basis of adaptive evolution in chemostats JO - FEMS Microbiol Rev VL - 39 ID - Gresham2014 ER - TY - JOUR AU - Bachmann, H. AU - Fischlechner, M. AU - Rabbers, I. AU - Barfa, N. AU - Branco dos Santos, F. AU - Molenaar, D. PY - 2013 DA - 2013// TI - Availability of public goods shapes the evolution of competing metabolic strategies JO - Proc Natl Acad Sci VL - 110 UR - https://doi.org/10.1073/pnas.1308523110 DO - 10.1073/pnas.1308523110 ID - Bachmann2013 ER - TY - JOUR AU - Meadows, A. L. AU - Karnik, R. AU - Lam, H. AU - Forestell, S. AU - Snedecor, B. PY - 2010 DA - 2010// TI - Application of dynamic flux balance analysis to an industrial Escherichia coli fermentation JO - Metab Eng VL - 12 UR - https://doi.org/10.1016/j.ymben.2009.07.006 DO - 10.1016/j.ymben.2009.07.006 ID - Meadows2010 ER - TY - STD TI - Novick A, Szilard L. Description of the Chemostat. Science. 1950;112(2920):715–6. ID - ref7 ER - TY - JOUR AU - Callens, C. AU - Coelho, N. C. AU - Miller, A. W. AU - Sananes, M. R. D. AU - Dunham, M. J. AU - Denoual, M. PY - 2017 DA - 2017// TI - A multiplex culture system for the long-term growth of fission yeast cells JO - Yeast VL - 34 UR - https://doi.org/10.1002/yea.3237 DO - 10.1002/yea.3237 ID - Callens2017 ER - TY - JOUR AU - Wegmann, U. AU - O’Connell-Motherway, M. AU - Zomer, A. AU - Buist, G. AU - Shearman, C. AU - Canchaya, C. PY - 2007 DA - 2007// TI - Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363 JO - J Bacteriol VL - 189 UR - https://doi.org/10.1128/JB.01768-06 DO - 10.1128/JB.01768-06 ID - Wegmann2007 ER - TY - JOUR AU - Bolotin, A. AU - Wincker, P. AU - Mauger, S. AU - Jaillon, O. AU - Malarme, K. AU - Weissenbach, J. PY - 2001 DA - 2001// TI - The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403 JO - Genome Res VL - 11 UR - https://doi.org/10.1101/gr.GR-1697R DO - 10.1101/gr.GR-1697R ID - Bolotin2001 ER - TY - JOUR AU - Makarova, K. AU - Slesarev, A. AU - Wolf, Y. AU - Sorokin, A. AU - Mirkin, B. AU - Koonin, E. PY - 2006 DA - 2006// TI - Comparative genomics of the lactic acid bacteria JO - Proc Natl Acad Sci VL - 103 UR - https://doi.org/10.1073/pnas.0607117103 DO - 10.1073/pnas.0607117103 ID - Makarova2006 ER - TY - JOUR AU - Siezen, R. J. AU - Bayjanov, J. AU - Renckens, B. AU - Wels, M. AU - Hijum, S. A. F. T. AU - Molenaar, D. PY - 2010 DA - 2010// TI - Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium JO - J Bacteriol VL - 192 UR - https://doi.org/10.1128/JB.00276-10 DO - 10.1128/JB.00276-10 ID - Siezen2010 ER - TY - JOUR AU - Jensen, P. R. AU - Hammer, K. PY - 1993 DA - 1993// TI - Minimal requirements for exponential growth of Lactococcus lactis JO - Appl Environ Microbiol VL - 59 ID - Jensen1993 ER - TY - JOUR AU - Oliveira, A. AU - Nielsen, J. AU - Förster, J. PY - 2005 DA - 2005// TI - Modeling Lactococcus lactis using a genome-scale flux model JO - BMC Microbiol VL - 15 ID - Oliveira2005 ER - TY - JOUR AU - Poolman, B. AU - Konings, W. N. PY - 1988 DA - 1988// TI - Relation of growth of Streptococcus lactis and Streptococcus cremoris to amino acid transport JO - J Bacteriol VL - 170 UR - https://doi.org/10.1128/jb.170.2.700-707.1988 DO - 10.1128/jb.170.2.700-707.1988 ID - Poolman1988 ER - TY - JOUR AU - Thomas, T. D. AU - Ellwood, D. C. AU - Longyear, V. M. PY - 1979 DA - 1979// TI - Change from homo- to heterolactic fermentation by Streptococcus lactis resulting from glucose limitation in anaerobic chemostat cultures JO - J Bacteriol VL - 138 ID - Thomas1979 ER - TY - JOUR AU - Linares, D. M. AU - Kok, J. AU - Poolman, B. PY - 2010 DA - 2010// TI - Genome sequences of Lactococcus lactis MG1363 (revised) and NZ9000 and comparative physiological studies JO - J Bacteriol VL - 192 UR - https://doi.org/10.1128/JB.00533-10 DO - 10.1128/JB.00533-10 ID - Linares2010 ER - TY - JOUR AU - Buist, G. AU - Kok, J. AU - Leenhouts, K. J. AU - Dabrowska, M. AU - Venema, G. AU - Haandrikman, A. J. PY - 1995 DA - 1995// TI - Molecular cloning and nucleotide sequence of the gene encoding the major peptidoglycan hydrolase of Lactococcus lactis, a muramidase needed for cell separation JO - J Bacteriol VL - 177 UR - https://doi.org/10.1128/jb.177.6.1554-1563.1995 DO - 10.1128/jb.177.6.1554-1563.1995 ID - Buist1995 ER - TY - JOUR AU - Barrick, J. E. AU - Yu, D. S. AU - Yoon, S. H. AU - Jeong, H. AU - Oh, T. K. AU - Schneider, D. PY - 2009 DA - 2009// TI - Genome evolution and adaptation in a long-term experiment with Escherichia coli JO - Nature VL - 461 UR - https://doi.org/10.1038/nature08480 DO - 10.1038/nature08480 ID - Barrick2009 ER - TY - JOUR AU - Kuipers, O. P. AU - Jong, A. AU - Baerends, R. J. S. AU - Hijum, S. A. F. T. AU - Zomer, A. L. AU - Karsens, H. A. PY - 2002 DA - 2002// TI - Transcriptome analysis and related databases of Lactococcus lactis JO - Antonie Van Leeuwenhoek VL - 82 UR - https://doi.org/10.1023/A:1020691801251 DO - 10.1023/A:1020691801251 ID - Kuipers2002 ER - TY - JOUR AU - Deutscher, J. AU - Francke, C. AU - Postma, P. W. PY - 2006 DA - 2006// TI - How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria JO - Microbiol Mol Biol Rev VL - 70 UR - https://doi.org/10.1128/MMBR.00024-06 DO - 10.1128/MMBR.00024-06 ID - Deutscher2006 ER - TY - JOUR AU - Castro, R. AU - Neves, A. R. AU - Fonseca, L. L. AU - Pool, W. A. AU - Kok, J. AU - Kuipers, O. P. PY - 2009 DA - 2009// TI - Characterization of the individual glucose uptake systems of Lactococcus lactis: mannose-PTS, cellobiose-PTS and the novel GlcU permease JO - Mol Microbiol VL - 71 UR - https://doi.org/10.1111/j.1365-2958.2008.06564.x DO - 10.1111/j.1365-2958.2008.06564.x ID - Castro2009 ER - TY - JOUR AU - Schumacher, M. A. AU - Sprehe, M. AU - Bartholomae, M. AU - Hillen, W. AU - Brennan, R. G. PY - 2011 DA - 2011// TI - Structures of carbon catabolite protein A-(HPr-Ser46-P) bound to diverse catabolite response element sites reveal the basis for high-affinity binding to degenerate DNA operators JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkq1177 DO - 10.1093/nar/gkq1177 ID - Schumacher2011 ER - TY - JOUR AU - Loll, B. AU - Kowalczyk, M. AU - Alings, C. AU - Chieduch, A. AU - Bardowski, J. AU - Saenger, W. PY - 2007 DA - 2007// TI - Structure of the transcription regulator CcpA from {\it Lactococcus lactis} JO - Acta Crystallogr Sect D VL - 63 UR - https://doi.org/10.1107/S0907444907000546 DO - 10.1107/S0907444907000546 ID - Loll2007 ER - TY - STD TI - Goel A, Eckhardt TH, Puri P, Jong A, Branco dos Santos F, Giera M, et al. Protein costs do not explain evolution of metabolic strategies and regulation of ribosomal content. Mol Microbiol. 2015;97(1):77–92. ID - ref25 ER - TY - JOUR AU - Marciniak, B. C. AU - Pabijaniak, M. AU - Jong, A. AU - Dűhring, R. AU - Seidel, G. AU - Hillen, W. PY - 2012 DA - 2012// TI - High- and low-affinity cre boxes for CcpA binding in Bacillus subtilis revealed by genome-wide analysis JO - BMC Genomics VL - 13 UR - https://doi.org/10.1186/1471-2164-13-401 DO - 10.1186/1471-2164-13-401 ID - Marciniak2012 ER - TY - JOUR AU - LaCroix, R. A. AU - Sandberg, T. E. AU - O’Brien, E. J. AU - Utrilla, J. AU - Ebrahim, A. AU - Guzman, G. I. PY - 2015 DA - 2015// TI - Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium JO - Appl Environ Microbiol VL - 81 UR - https://doi.org/10.1128/AEM.02246-14 DO - 10.1128/AEM.02246-14 ID - LaCroix2015 ER - TY - JOUR AU - Utrilla, J. AU - O’Brien, E. J. AU - Chen, K. AU - McCloskey, D. AU - Cheung, J. AU - Wang, H. PY - 2016 DA - 2016// TI - Global rebalancing of cellular resources by pleiotropic point mutations illustrates a multi-scale mechanism of adaptive evolution JO - Cell Syst VL - 2 UR - https://doi.org/10.1016/j.cels.2016.04.003 DO - 10.1016/j.cels.2016.04.003 ID - Utrilla2016 ER - TY - JOUR AU - Moxley, J. F. AU - Jewett, M. C. AU - Antoniewicz, M. R. AU - Villas-Boas, S. G. AU - Alper, H. AU - Wheeler, R. T. PY - 2009 DA - 2009// TI - Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p JO - Proc Natl Acad Sci VL - 106 UR - https://doi.org/10.1073/pnas.0811091106 DO - 10.1073/pnas.0811091106 ID - Moxley2009 ER - TY - JOUR AU - Kowalczyk, M. AU - Bardowski, J. PY - 2003 DA - 2003// TI - Overproduction and purification of the CcpA protein from Lactococcus lactis JO - Acta Biochim Pol VL - 50 ID - Kowalczyk2003 ER - TY - JOUR AU - Hijum, S. A. F. T. AU - Jong, A. AU - Buist, G. AU - Kok, J. AU - Kuipers, O. P. PY - 2003 DA - 2003// TI - UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons JO - Bioinforma VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg203 DO - 10.1093/bioinformatics/btg203 ID - Hijum2003 ER - TY - JOUR AU - Hijum, S. AU - Jong, A. AU - Baerends, R. AU - Karsens, H. AU - Kramer, N. AU - Larsen, R. PY - 2005 DA - 2005// TI - A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data JO - BMC Genomics VL - 6 UR - https://doi.org/10.1186/1471-2164-6-77 DO - 10.1186/1471-2164-6-77 ID - Hijum2005 ER - TY - JOUR AU - Hochberg, Y. AU - Benjamini, Y. PY - 1990 DA - 1990// TI - More powerful procedures for multiple significance testing JO - Stat Med VL - 9 UR - https://doi.org/10.1002/sim.4780090710 DO - 10.1002/sim.4780090710 ID - Hochberg1990 ER - TY - JOUR AU - Breitling, R. AU - Armengaud, P. AU - Amtmann, A. AU - Herzyk, P. PY - 2004 DA - 2004// TI - Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments JO - FEBS Lett VL - 573 UR - https://doi.org/10.1016/j.febslet.2004.07.055 DO - 10.1016/j.febslet.2004.07.055 ID - Breitling2004 ER - TY - JOUR AU - Jong, A. AU - Pietersma, H. AU - Cordes, M. AU - Kuipers, O. AU - Kok, J. PY - 2012 DA - 2012// TI - PePPER: a webserver for prediction of prokaryote promoter elements and regulons JO - BMC Genomics VL - 13 UR - https://doi.org/10.1186/1471-2164-13-299 DO - 10.1186/1471-2164-13-299 ID - Jong2012 ER - TY - JOUR AU - Gouridis, G. AU - Schuurman-Wolters, G. K. AU - Ploetz, E. AU - Husada, F. AU - Vietrov, R. AU - Boer, M. PY - 2015 DA - 2015// TI - Conformational dynamics in substrate-binding domains influences transport in the ABC importer GlnPQ JO - Nat Struct Mol Biol VL - 22 UR - https://doi.org/10.1038/nsmb.2929 DO - 10.1038/nsmb.2929 ID - Gouridis2015 ER - TY - JOUR AU - Arnold, K. AU - Bordoli, L. AU - Kopp, J. AU - Schwede, T. PY - 2006 DA - 2006// TI - The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling JO - Bioinforma VL - 22 UR - https://doi.org/10.1093/bioinformatics/bti770 DO - 10.1093/bioinformatics/bti770 ID - Arnold2006 ER - TY - JOUR AU - Hess, B. AU - Kutzner, C. AU - Spoel, D. AU - Lindahl, E. PY - 2008 DA - 2008// TI - GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation JO - J Chem Theory Comput VL - 4 UR - https://doi.org/10.1021/ct700301q DO - 10.1021/ct700301q ID - Hess2008 ER - TY - JOUR AU - Foloppe, N. AU - MacKerell, A. D. PY - 2000 DA - 2000// TI - All-atom empirical force field for nucleic acids: I. parameter optimization based on small molecule and condensed phase macromolecular target data JO - J Comput Chem VL - 21 UR - https://doi.org/3.0.CO;2-G DO - 3.0.CO;2-G ID - Foloppe2000 ER - TY - JOUR AU - MacKerell, A. D. AU - Feig, M. AU - Brooks, C. L. PY - 2004 DA - 2004// TI - Improved treatment of the protein backbone in empirical force fields JO - J Am Chem Soc VL - 126 UR - https://doi.org/10.1021/ja036959e DO - 10.1021/ja036959e ID - MacKerell2004 ER - TY - JOUR AU - Jorgensen, W. L. AU - Chandrasekhar, J. AU - Madura, J. D. AU - Impey, R. W. AU - Klein, M. L. PY - 1983 DA - 1983// TI - Comparison of simple potential functions for simulating liquid water JO - J Chem Phys VL - 79 UR - https://doi.org/10.1063/1.445869 DO - 10.1063/1.445869 ID - Jorgensen1983 ER - TY - JOUR AU - Bennett, C. H. PY - 1976 DA - 1976// TI - Efficient estimation of free energy differences from Monte Carlo data JO - J Comput Phys VL - 22 UR - https://doi.org/10.1016/0021-9991(76)90078-4 DO - 10.1016/0021-9991(76)90078-4 ID - Bennett1976 ER - TY - JOUR AU - Ashkenazy, H. AU - Erez, E. AU - Martz, E. AU - Pupko, T. AU - Ben-Tal, N. PY - 2010 DA - 2010// TI - ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkq399 DO - 10.1093/nar/gkq399 ID - Ashkenazy2010 ER -