title: Protein costs do not explain evolution of metabolic strategies and regulation of ribosomal content: does protein investment explain an anaerobic bacterial Crabtree effect?
abstract: Protein investment costs are considered a major driver for the choice of alternative metabolic strategies. We tested this premise in Lactococcus lactis, a bacterium that exhibits a distinct, anaerobic version of the bacterial Crabtree/Warburg effect; with increasing growth rates it shifts from a high yield metabolic mode [mixed-acid fermentation; 3 adenosine triphosphate (ATP) per glucose] to a low yield metabolic mode (homolactic fermentation; 2 ATP per glucose). We studied growth rate-dependent relative transcription and protein ratios, enzyme activities, and fluxes of L. lactis in glucose-limited chemostats, providing a high-quality and comprehensive data set. A three- to fourfold higher growth rate rerouted metabolism from acetate to lactate as the main fermentation product. However, we observed hardly any changes in transcription, protein levels and enzyme activities. Even levels of ribosomal proteins, constituting a major investment in cellular machinery, changed only slightly. Thus, contrary to the original hypothesis, central metabolism in this organism appears to be hardly regulated at the level of gene expression, but rather at the metabolic level. We conclude that L. lactis is either poorly adapted to growth at low and constant glucose concentrations, or that protein costs play a less important role in fitness than hitherto assumed.
authors.affiliation: Systems Bioinformatics IBIVU, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.|Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands.|Kluyver Centre for Genomics of Industrial Fermentation/Netherlands consortium for Systems Biology (NCSB), P.O. Box 5057, 2600 GA, Delft, The Netherlands.
authors.forename: Anisha
authors.initials: A
authors.lastname: Goel
authors.affiliation: Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Netherlands Proteomics Centre and Zernike Institute for Advanced Materials (ZIAM), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
authors.forename: Thomas H
authors.initials: TH
authors.lastname: Eckhardt
authors.affiliation: Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Netherlands Proteomics Centre and Zernike Institute for Advanced Materials (ZIAM), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
authors.forename: Pranav
authors.initials: P
authors.lastname: Puri
authors.affiliation: Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Netherlands Proteomics Centre and Zernike Institute for Advanced Materials (ZIAM), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
authors.forename: Anne
authors.initials: A
authors.lastname: de Jong
authors.affiliation: Systems Bioinformatics IBIVU, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.|Kluyver Centre for Genomics of Industrial Fermentation/Netherlands consortium for Systems Biology (NCSB), P.O. Box 5057, 2600 GA, Delft, The Netherlands.
authors.forename: Filipe
authors.initials: F
authors.lastname: Branco Dos Santos
authors.affiliation: Systems Bioinformatics IBIVU, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
authors.forename: Martin
authors.initials: M
authors.lastname: Giera
authors.affiliation: Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Netherlands Proteomics Centre and Zernike Institute for Advanced Materials (ZIAM), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
authors.forename: Fabrizia
authors.initials: F
authors.lastname: Fusetti
authors.affiliation: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands.
authors.forename: Willem M
authors.initials: WM
authors.lastname: de Vos
authors.affiliation: Kluyver Centre for Genomics of Industrial Fermentation/Netherlands consortium for Systems Biology (NCSB), P.O. Box 5057, 2600 GA, Delft, The Netherlands.|Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Netherlands Proteomics Centre and Zernike Institute for Advanced Materials (ZIAM), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
authors.forename: Jan
authors.initials: J
authors.lastname: Kok
authors.affiliation: Kluyver Centre for Genomics of Industrial Fermentation/Netherlands consortium for Systems Biology (NCSB), P.O. Box 5057, 2600 GA, Delft, The Netherlands.|Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Netherlands Proteomics Centre and Zernike Institute for Advanced Materials (ZIAM), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
authors.forename: Bert
authors.initials: B
authors.lastname: Poolman
authors.affiliation: Systems Bioinformatics IBIVU, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.|Kluyver Centre for Genomics of Industrial Fermentation/Netherlands consortium for Systems Biology (NCSB), P.O. Box 5057, 2600 GA, Delft, The Netherlands.
authors.forename: Douwe
authors.initials: D
authors.lastname: Molenaar
authors.affiliation: Kluyver Centre for Genomics of Industrial Fermentation/Netherlands consortium for Systems Biology (NCSB), P.O. Box 5057, 2600 GA, Delft, The Netherlands.|Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Netherlands Proteomics Centre and Zernike Institute for Advanced Materials (ZIAM), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
authors.forename: Oscar P
authors.initials: OP
authors.lastname: Kuipers
authors.affiliation: Systems Bioinformatics IBIVU, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.|Kluyver Centre for Genomics of Industrial Fermentation/Netherlands consortium for Systems Biology (NCSB), P.O. Box 5057, 2600 GA, Delft, The Netherlands.
authors.forename: Bas
authors.initials: B
authors.lastname: Teusink
mesh_terms: D000085:Acetates / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D001120:Arginine / Q000378:metabolism; D001421:Bacteria, Anaerobic / Q000378:metabolism; D005285:Fermentation; D005947:Glucose / Q000378:metabolism*; D006019:Glycolysis; D007700:Kinetics; D019344:Lactic Acid / Q000378:metabolism; D013294:Lactococcus lactis / Q000201:enzymology / Q000235:genetics / Q000254:growth & development* / Q000378:metabolism*; D012269:Ribosomal Proteins / Q000096:biosynthesis / Q000378:metabolism*; D012270:Ribosomes / Q000378:metabolism*
chemical_list: D000085:Acetates; D012269:Ribosomal Proteins; D019344:Lactic Acid; D000255:Adenosine Triphosphate; D001120:Arginine; D005947:Glucose