Adaptively evolved yeast mutants on galactose show trade-offs in carbon utilization on glucose

Metabolic Engineering

Volumn 16, Issue 1, 2013, Pages 78-86

  Hong, Kuk Ki ^a,b   Nielsen, Jens ^a,c  

^a CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

^b CJ Corporation   (South Korea)

^c Chalmers University of Technology   (Denmark)

Author keywords

Evolutionary trade off; Galactose metabolism; Glucose regulation; Metabolic engineering; Ras PKA signaling pathway; Systems biology

Indexed keywords

EVOLUTIONARY TRADE-OFF; GALACTOSE METABOLISM; GLUCOSE REGULATION; SIGNALING PATHWAYS; SYSTEMS BIOLOGY;

ECONOMIC AND SOCIAL EFFECTS; GENE EXPRESSION; METABOLIC ENGINEERING; PLANTS (BOTANY); YEAST;

GLUCOSE;

GALACTOSE; GLUCOSE;

ARTICLE; CARBOHYDRATE METABOLISM; CONTROLLED STUDY; EVOLUTION; FUNGUS GROWTH; GENE MUTATION; GLUCOSE UTILIZATION; MOLECULAR GENETICS; NONHUMAN; PLEIOTROPY; PRIORITY JOURNAL; PROTEIN EXPRESSION; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION REGULATION;

CARBON; CLONAL EVOLUTION; GALACTOSE; GLUCOSE; MUTATION; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EID: 84874284372     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2013.01.007     Document Type: Article

References (27)

1. Bennett A.F., Hughes B.S. Microbial experimental evolution. Am. J. Physiol. Regul. Integr. Comput. Physiol. 2009, 297:R17-R25.
2. Bennett A.F., Lenski R.E. An experimental test of evolutionary trade-offs during temperature adaptation. Proc. Nat. Acad. Sci. U.S.A. 2007, 104(Suppl 1):8649-8654.
3. Bro C., Knudsen S., Regenberg B., Olsson L., Nielsen J. Improvement of galactose uptake in Saccharomyces cerevisiae through overexpression of phosphoglucomutase: example of transcript analysis as a tool in inverse metabolic engineering. Appl. Environ. Microbiol. 2005, 71:6465-6472.
4. Bro C., Nielsen J. Impact of 'ome' analyses on inverse metabolic engineering. Metab. Eng. 2004, 6:204-211.
5. Chang S.L., Leu J.Y. A tradeoff drives the evolution of reduced metal resistance in natural populations of yeast. PLos Genet. 2011, 7:e1002034.
6. Conrad T.M., Frazier M., Joyce A.R., Cho B.K., Knight E.M., Lewis N.E., Landick R., Palsson B.O. RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media. Proc. Nat. Acad. Sci. U.S.A. 2010, 107:20500-20505.
7. Conrad T.M., Lewis N.E., Palsson B.O. Microbial laboratory evolution in the era of genome-scale science. Mol. Syst. Biol. 2011, 7:509.
8. Cooper V.S., Lenski R.E. The population genetics of ecological specialization in evolving Escherichia coli populations. Nature 2000, 407:736-739.
9. Daran-Lapujade P., Rossell S., van Gulik W.M., Luttik M.A., de Groot M.J., Slijper M., Heck A.J., Daran J.M., de Winde J.H., Westerhoff H.V., Pronk J.T., Bakker B.M. The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels. Proc. Nat. Acad. Sci. USA 2007, 104:15753-15758.
10. Dettman J.R., Rodrigue N., Melnyk A.H., Wong A., Bailey S.F., Kassen R. Evolutionary insight from whole-genome sequencing of experimentally evolved microbes. Mol. Ecol. 2012, 21:2058-2077.
11. Elena S.F., Lenski R.E. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat. Rev. Genet. 2003, 4:457-469.
12. Herring C.D., Raghunathan A., Honisch C., Patel T., Applebee M.K., Joyce A.R., Albert T.J., Blattner F.R., van den Boom D., Cantor C.R., Palsson B.O. Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat. Genet. 2006, 38:1406-1412.
13. Hong K.K., Nielsen J. Recovery of phenotypes obtained by adaptive evolution through inverse metabolic engineering. Appl. Environ. Microbiol. 2012, 78:7579-7586.
14. Hong K.K., Vongsangnak W., Vemuri G.N., Nielsen J. Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis. Proc. Nat. Acad. Sci. U.S.A. 2011, 108:12179-12184.
15. Kao K.C., Sherlock G. Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae. Nat. Genet. 2008, 40:1499-1504.
16. Khan A.I., Dinh D.M., Schneider D., Lenski R.E., Cooper T.F. Negative epistasis between beneficial mutations in an evolving bacterial population. Science 2011, 332:1193-1196.
17. Kvitek D.J., Sherlock G. Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape. PLos Genet. 2011, 7:e1002056.
18. Lee K.S., Hong M.E., Jung S.C., Ha S.J., Yu B.J., Koo H.M., Park S.M., Seo J.H., Kweon D.H., Park J.C., Jin Y.S. Improved galactose fermentation of Saccharomyces cerevisiae through inverse metabolic engineering. Biotechnol. Bioeng. 2011, 108:621-631.
19. Orzechowski Westholm J., Tronnersjo S., Nordberg N., Olsson I., Komorowski J., Ronne H. Gis1 and Rph1 regulate glycerol and acetate metabolism in glucose depleted yeast cells. PLoS One 2012, 7:e31577.
20. Ostergaard S., Olsson L., Johnston M., Nielsen J. Increasing galactose consumption by Saccharomyces cerevisiae through metabolic engineering of the GAL gene regulatory network. Nat. Biotechnol. 2000, 18:1283-1286.
21. Reimand J., Arak T., Vilo J. g:Profiler-a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Res. 2011, 39:W307-W315.
22. Rodriguez A., De La Cera T., Herrero P., Moreno F. The hexokinase 2 protein regulates the expression of the GLK1, HXK1 and HXK2 genes of Saccharomyces cerevisiae. Biochem. J. 2001, 355:625-631.
23. Saeed A.I., Sharov V., White J., Li J., Liang W., Bhagabati N., Braisted J., Klapa M., Currier T., Thiagarajan M., Sturn A., Snuffin M., Rezantsev A., Popov D., Ryltsov A., Kostukovich E., Borisovsky I., Liu Z., Vinsavich A., Trush V., Quackenbush J. TM4: a free, open-source system for microarray data management and analysis. Biotechniques 2003, 34:374-378.
24. Smith K.M., Liao J.C. An evolutionary strategy for isobutanol production strain development in Escherichia coli. Metab. Eng. 2011, 13:674-681.
25. Tamaki H. Glucose-stimulated cAMP-protein kinase a pathway in yeast Saccharomyces cerevisiae. J. Biosci. Bioeng. 2007, 104:245-250.
26. Wenger J.W., Piotrowski J., Nagarajan S., Chiotti K., Sherlock G., Rosenzweig F. Hunger artists: yeast adapted to carbon limitation show trade-offs under carbon sufficiency. PLoS Genet. 2011, 7.
27. Zhou H., Winston F. NRG1 is required for glucose repression of the SUC2 and GAL genes of Saccharomyces cerevisiae. BMC Genet. 2001, 2:5.