Biosensor-driven adaptive laboratory evolution of L-valine production in Corynebacterium glutamicum

Mahr R, Gaetgens C, Gaetgens J, Polen T, Kalinowski J, Frunzke J (2015)
Metabolic Engineering 32: 184-194.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Mahr, Regina; Gaetgens, Cornelia; Gaetgens, Jochem; Polen, Tino; Kalinowski, JörnUniBi; Frunzke, Julia
Abstract / Bemerkung
Adaptive laboratory evolution has proven a valuable strategy for metabolic engineering. Here, we established an experimental evolution approach for improving microbial metabolite production by imposing an artificial selective pressure on the fluorescent output of a biosensor using fluorescence-activated cell sorting. Cells showing the highest fluorescent output were iteratively isolated and (re-) cultivated. The L-valine producer Corynebacterium glutamicum Delta aceE was equipped with an L-valine-responsive sensor based on the transcriptional regulator Lrp of C. glutamicum. Evolved strains featured a significantly higher growth rate, increased L-valine titers (similar to 25%) and a 3-4-fold reduction of by-product formation. Genome sequencing resulted in the identification of a loss-of-function mutation (UreD-E188*) in the gene ureD (urease accessory protein), which was shown to increase L-valine production by up to 100%. Furthermore, decreased L-alanine formation was attributed to a mutation in the global regulator GlxR. These results emphasize biosensor-driven evolution as a straightforward approach to improve growth and productivity of microbial production strains. (C) 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.
Stichworte
Biosensor
Erscheinungsjahr
2015
Zeitschriftentitel
Metabolic Engineering
Band
32
Seite(n)
184-194
ISSN
1096-7176
eISSN
1096-7184
Page URI
https://pub.uni-bielefeld.de/record/2901032

Zitieren

Mahr R, Gaetgens C, Gaetgens J, Polen T, Kalinowski J, Frunzke J. Biosensor-driven adaptive laboratory evolution of L-valine production in Corynebacterium glutamicum. Metabolic Engineering. 2015;32:184-194.
Mahr, R., Gaetgens, C., Gaetgens, J., Polen, T., Kalinowski, J., & Frunzke, J. (2015). Biosensor-driven adaptive laboratory evolution of L-valine production in Corynebacterium glutamicum. Metabolic Engineering, 32, 184-194. doi:10.1016/j.ymben.2015.09.017
Mahr, R., Gaetgens, C., Gaetgens, J., Polen, T., Kalinowski, J., and Frunzke, J. (2015). Biosensor-driven adaptive laboratory evolution of L-valine production in Corynebacterium glutamicum. Metabolic Engineering 32, 184-194.
Mahr, R., et al., 2015. Biosensor-driven adaptive laboratory evolution of L-valine production in Corynebacterium glutamicum. Metabolic Engineering, 32, p 184-194.
R. Mahr, et al., “Biosensor-driven adaptive laboratory evolution of L-valine production in Corynebacterium glutamicum”, Metabolic Engineering, vol. 32, 2015, pp. 184-194.
Mahr, R., Gaetgens, C., Gaetgens, J., Polen, T., Kalinowski, J., Frunzke, J.: Biosensor-driven adaptive laboratory evolution of L-valine production in Corynebacterium glutamicum. Metabolic Engineering. 32, 184-194 (2015).
Mahr, Regina, Gaetgens, Cornelia, Gaetgens, Jochem, Polen, Tino, Kalinowski, Jörn, and Frunzke, Julia. “Biosensor-driven adaptive laboratory evolution of L-valine production in Corynebacterium glutamicum”. Metabolic Engineering 32 (2015): 184-194.

30 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

In vivo biosensors: mechanisms, development, and applications.
Shi S, Ang EL, Zhao H., J Ind Microbiol Biotechnol 45(7), 2018
PMID: 29380152
A protocatechuate biosensor for Pseudomonas putida KT2440 via promoter and protein evolution.
Jha RK, Bingen JM, Johnson CW, Kern TL, Khanna P, Trettel DS, Strauss CEM, Beckham GT, Dale T., Metab Eng Commun 6(), 2018
PMID: 29765865
Promoter library-based module combination (PLMC) technology for optimization of threonine biosynthesis in Corynebacterium glutamicum.
Wei L, Xu N, Wang Y, Zhou W, Han G, Ma Y, Liu J., Appl Microbiol Biotechnol 102(9), 2018
PMID: 29564525
Production of L-valine from metabolically engineered Corynebacterium glutamicum.
Wang X, Zhang H, Quinn PJ., Appl Microbiol Biotechnol 102(10), 2018
PMID: 29594358
Evolutionary engineering of industrial microorganisms-strategies and applications.
Zhu Z, Zhang J, Ji X, Fang Z, Wu Z, Chen J, Du G., Appl Microbiol Biotechnol 102(11), 2018
PMID: 29623387
Development of N-acetylneuraminic acid responsive biosensors based on the transcriptional regulator NanR.
Peters G, De Paepe B, De Wannemaeker L, Duchi D, Maertens J, Lammertyn J, De Mey M., Biotechnol Bioeng 115(7), 2018
PMID: 29532902
Genome shuffling and high-throughput screening of Brevibacterium flavum MDV1 for enhanced L-valine production.
Huang QG, Zeng BD, Liang L, Wu SG, Huang JZ., World J Microbiol Biotechnol 34(8), 2018
PMID: 30039311
Blueprints for Biosensors: Design, Limitations, and Applications.
Carpenter AC, Paulsen IT, Williams TC., Genes (Basel) 9(8), 2018
PMID: 30050028
Enhanced Metabolite Productivity of Escherichia coli Adapted to Glucose M9 Minimal Medium.
Rugbjerg P, Feist AM, Sommer MOA., Front Bioeng Biotechnol 6(), 2018
PMID: 30483499
NADPH-related processes studied with a SoxR-based biosensor in Escherichia coli.
Spielmann A, Baumgart M, Bott M., Microbiologyopen (), 2018
PMID: 30585443
Tailor-made transcriptional biosensors for optimizing microbial cell factories.
De Paepe B, Peters G, Coussement P, Maertens J, De Mey M., J Ind Microbiol Biotechnol 44(4-5), 2017
PMID: 27837353
Systems biology solutions for biochemical production challenges.
Hansen ASL, Lennen RM, Sonnenschein N, Herrgård MJ., Curr Opin Biotechnol 45(), 2017
PMID: 28319856
High precision genome sequencing of engineered Gluconobacter oxydans 621H by combining long nanopore and short accurate Illumina reads.
Kranz A, Vogel A, Degner U, Kiefler I, Bott M, Usadel B, Polen T., J Biotechnol 258(), 2017
PMID: 28433722
Miniaturized and automated adaptive laboratory evolution: Evolving Corynebacterium glutamicum towards an improved d-xylose utilization.
Radek A, Tenhaef N, Müller MF, Brüsseler C, Wiechert W, Marienhagen J, Polen T, Noack S., Bioresour Technol 245(pt b), 2017
PMID: 28552568
Systems metabolic engineering strategies for the production of amino acids.
Ma Q, Zhang Q, Xu Q, Zhang C, Li Y, Fan X, Xie X, Chen N., Synth Syst Biotechnol 2(2), 2017
PMID: 29062965
A real-time control system of gene expression using ligand-bound nucleic acid aptamer for metabolic engineering.
Wang J, Cui X, Yang L, Zhang Z, Lv L, Wang H, Zhao Z, Guan N, Dong L, Chen R., Metab Eng 42(), 2017
PMID: 28603040
Sense and sensitivity in bioprocessing-detecting cellular metabolites with biosensors.
Dekker L, Polizzi KM., Curr Opin Chem Biol 40(), 2017
PMID: 28609710
Homogenizing bacterial cell factories: Analysis and engineering of phenotypic heterogeneity.
Binder D, Drepper T, Jaeger KE, Delvigne F, Wiechert W, Kohlheyer D, Grünberger A., Metab Eng 42(), 2017
PMID: 28645641
Assessing glycolytic flux alterations resulting from genetic perturbations in E. coli using a biosensor.
Lehning CE, Siedler S, Ellabaan MMH, Sommer MOA., Metab Eng 42(), 2017
PMID: 28709932
Biosensor-Enabled Directed Evolution to Improve Muconic Acid Production in Saccharomyces cerevisiae.
Leavitt JM, Wagner JM, Tu CC, Tong A, Liu Y, Alper HS., Biotechnol J 12(10), 2017
PMID: 28296355
Engineering Robustness of Microbial Cell Factories.
Gong Z, Nielsen J, Zhou YJ., Biotechnol J 12(10), 2017
PMID: 28857502
SensiPath: computer-aided design of sensing-enabling metabolic pathways.
Delépine B, Libis V, Carbonell P, Faulon JL., Nucleic Acids Res 44(w1), 2016
PMID: 27106061
Recent advances in amino acid production by microbial cells.
Hirasawa T, Shimizu H., Curr Opin Biotechnol 42(), 2016
PMID: 27151315
Screening of an Escherichia coli promoter library for a phenylalanine biosensor.
Mahr R, von Boeselager RF, Wiechert J, Frunzke J., Appl Microbiol Biotechnol 100(15), 2016
PMID: 27170323
Light-Controlled Cell Factories: Employing Photocaged Isopropyl-β-d-Thiogalactopyranoside for Light-Mediated Optimization of lac Promoter-Based Gene Expression and (+)-Valencene Biosynthesis in Corynebacterium glutamicum.
Binder D, Frohwitter J, Mahr R, Bier C, Grünberger A, Loeschcke A, Peters-Wendisch P, Kohlheyer D, Pietruszka J, Frunzke J, Jaeger KE, Wendisch VF, Drepper T., Appl Environ Microbiol 82(20), 2016
PMID: 27520809

72 References

Daten bereitgestellt von Europe PubMed Central.

Expanding the metabolic engineering toolbox with directed evolution.
Abatemarco J, Hill A, Alper HS., Biotechnol J 8(12), 2013
PMID: 23857895
Engineering yeast transcription machinery for improved ethanol tolerance and production.
Alper H, Moxley J, Nevoigt E, Fink GR, Stephanopoulos G., Science 314(5805), 2006
PMID: 17158319
Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli.
Atsumi S, Wu TY, Machado IM, Huang WC, Chen PY, Pellegrini M, Liao JC., Mol. Syst. Biol. 6(), 2010
PMID: 21179021
Genome dynamics during experimental evolution.
Barrick JE, Lenski RE., Nat. Rev. Genet. 14(12), 2013
PMID: 24166031
IpsA, a novel LacI-type regulator, is required for inositol-derived lipid formation in Corynebacteria and Mycobacteria.
Baumgart M, Luder K, Grover S, Gatgens C, Besra GS, Frunzke J., BMC Biol. 11(), 2013
PMID: 24377418
A high-throughput approach to identify genomic variants of bacterial metabolite producers at the single-cell level.
Binder S, Schendzielorz G, Stabler N, Krumbach K, Hoffmann K, Bott M, Eggeling L., Genome Biol. 13(5), 2012
PMID: 22640862
Impact of different CO2/HCO3- levels on metabolism and regulation in Corynebacterium glutamicum.
Blombach B, Buchholz J, Busche T, Kalinowski J, Takors R., J. Biotechnol. 168(4), 2013
PMID: 24140290
Corynebacterium glutamicum tailored for high-yield L-valine production.
Blombach B, Schreiner ME, Bartek T, Oldiges M, Eikmanns BJ., Appl. Microbiol. Biotechnol. 79(3), 2008
PMID: 18379776
L-valine production with pyruvate dehydrogenase complex-deficient Corynebacterium glutamicum.
Blombach B, Schreiner ME, Holatko J, Bartek T, Oldiges M, Eikmanns BJ., Appl. Environ. Microbiol. 73(7), 2007
PMID: 17293513
Platform engineering of Corynebacterium glutamicum with reduced pyruvate dehydrogenase complex activity for improved production of L-lysine, L-valine, and 2-ketoisovalerate.
Buchholz J, Schwentner A, Brunnenkan B, Gabris C, Grimm S, Gerstmeir R, Takors R, Eikmanns BJ, Blombach B., Appl. Environ. Microbiol. 79(18), 2013
PMID: 23835179
Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction.
Charusanti P, Fong NL, Nagarajan H, Pereira AR, Li HJ, Abate EA, Su Y, Gerwick WH, Palsson BO., PLoS ONE 7(3), 2012
PMID: 22470465
Metabolic engineering of Corynebacterium glutamicum ATCC13869 for L-valine production.
Chen C, Li Y, Hu J, Dong X, Wang X., Metab. Eng. 29(), 2015
PMID: 25769288
Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol.
Cheng KK, Lee BS, Masuda T, Ito T, Ikeda K, Hirayama A, Deng L, Dong J, Shimizu K, Soga T, Tomita M, Palsson BO, Robert M., Nat Commun 5(), 2014
PMID: 24481126
Programming adaptive control to evolve increased metabolite production.
Chou HH, Keasling JD., Nat Commun 4(), 2013
PMID: 24131951
The art of strain improvement of industrial lactic acid bacteria without the use of recombinant DNA technology.
Derkx PM, Janzen T, Sorensen KI, Christensen JE, Stuer-Lauridsen B, Johansen E., Microb. Cell Fact. 13 Suppl 1(), 2014
PMID: 25186244
High-throughput metabolic engineering: advances in small-molecule screening and selection.
Dietrich JA, McKee AE, Keasling JD., Annu. Rev. Biochem. 79(), 2010
PMID: 20367033
Transcription factor-based screens and synthetic selections for microbial small-molecule biosynthesis.
Dietrich JA, Shis DL, Alikhani A, Keasling JD., ACS Synth Biol 2(1), 2012
PMID: 23656325
Programmed evolution for optimization of orthogonal metabolic output in bacteria.
Eckdahl TT, Campbell AM, Heyer LJ, Poet JL, Blauch DN, Snyder NL, Atchley DT, Baker EJ, Brown M, Brunner EC, Callen SA, Campbell JS, Carr CJ, Carr DR, Chadinha SA, Chester GI, Chester J, Clarkson BR, Cochran KE, Doherty SE, Doyle C, Dwyer S, Edlin LM, Evans RA, Fluharty T, Frederick J, Galeota-Sprung J, Gammon BL, Grieshaber B, Gronniger J, Gutteridge K, Henningsen J, Isom B, Itell HL, Keffeler EC, Lantz AJ, Lim JN, McGuire EP, Moore AK, Morton J, Nakano M, Pearson SA, Perkins V, Parrish P, Pierson CE, Polpityaarachchige S, Quaney MJ, Slattery A, Smith KE, Spell J, Spencer M, Taye T, Trueblood K, Vrana CJ, Whitesides ET., PLoS ONE 10(2), 2015
PMID: 25714374

Eggeling, 2005
Novel screening methods-biosensors
Eggeling, Curr. Opin. Biotechnol. 35C(), 2015

AUTHOR UNKNOWN, 0
Nucleotide sequence, expression and transcriptional analysis of the Corynebacterium glutamicum gltA gene encoding citrate synthase.
Eikmanns BJ, Thum-Schmitz N, Eggeling L, Ludtke KU, Sahm H., Microbiology (Reading, Engl.) 140 ( Pt 8)(), 1994
PMID: 7522844
Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli.
Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BO., Metab. Eng. 12(3), 2009
PMID: 19840862
In silico design and adaptive evolution of Escherichia coli for production of lactic acid.
Fong SS, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson BO., Biotechnol. Bioeng. 91(5), 2005
PMID: 15962337
Enzymatic assembly of DNA molecules up to several hundred kilobases.
Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA 3rd, Smith HO., Nat. Methods 6(5), 2009
PMID: 19363495
An efficient random mutagenesis technique using an E. coli mutator strain.
Greener A, Callahan M, Jerpseth B., Mol. Biotechnol. 7(2), 1997
PMID: 9219234
Studies on transformation of Escherichia coli with plasmids.
Hanahan D., J. Mol. Biol. 166(4), 1983
PMID: 6345791
Improvement of the redox balance increases L-valine production by Corynebacterium glutamicum under oxygen deprivation conditions.
Hasegawa S, Uematsu K, Natsuma Y, Suda M, Hiraga K, Jojima T, Inui M, Yukawa H., Appl. Environ. Microbiol. 78(3), 2011
PMID: 22138982
Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale.
Herring CD, Raghunathan A, Honisch C, Patel T, Applebee MK, Joyce AR, Albert TJ, Blattner FR, van den Boom D, Cantor CR, Palsson BO., Nat. Genet. 38(12), 2006
PMID: 17086184
Adaptation of yeast cell membranes to ethanol.
Jimenez J, Benitez T., Appl. Environ. Microbiol. 53(5), 1987
PMID: 16347349
High-resolution detection of DNA binding sites of the global transcriptional regulator GlxR in Corynebacterium glutamicum.
Jungwirth B, Sala C, Kohl TA, Uplekar S, Baumbach J, Cole ST, Puhler A, Tauch A., Microbiology (Reading, Engl.) 159(Pt 1), 2012
PMID: 23103979
The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins.
Kalinowski J, Bathe B, Bartels D, Bischoff N, Bott M, Burkovski A, Dusch N, Eggeling L, Eikmanns BJ, Gaigalat L, Goesmann A, Hartmann M, Huthmacher K, Kramer R, Linke B, McHardy AC, Meyer F, Mockel B, Pfefferle W, Puhler A, Rey DA, Ruckert C, Rupp O, Sahm H, Wendisch VF, Wiegrabe I, Tauch A., J. Biotechnol. 104(1-3), 2003
PMID: 12948626
Studies on the amino acid fermentation. Part 1. Production of L-glutamic acid by various microorganisms.
Kinoshita S, Udaka S, Shimono M., J. Gen. Appl. Microbiol. 50(6), 2004
PMID: 15965888
Lrp of Corynebacterium glutamicum controls expression of the brnFE operon encoding the export system for L-methionine and branched-chain amino acids.
Lange C, Mustafi N, Frunzke J, Kennerknecht N, Wessel M, Bott M, Wendisch VF., J. Biotechnol. 158(4), 2011
PMID: 21683740
Engineering butanol-tolerance in escherichia coli with artificial transcription factor libraries.
Lee JY, Yang KS, Jang SA, Sung BH, Kim SC., Biotechnol. Bioeng. 108(4), 2010
PMID: 21404248

AUTHOR UNKNOWN, 0
Genomic adaptation of ethanologenic yeast to biomass conversion inhibitors.
Liu ZL., Appl. Microbiol. Biotechnol. 73(1), 2006
PMID: 17028874
Adaptive laboratory evolution of Escherichia coli K-12 MG1655 for growth at high hydrostatic pressure.
Marietou A, Nguyen AT, Allen EE, Bartlett DH., Front Microbiol 5(), 2014
PMID: 25610434
Genetically-encoded biosensors for strain development and single cell analysis of Corynebacterium glutamicum
Mustafi, 2015
The development and application of a single-cell biosensor for the detection of l-methionine and branched-chain amino acids.
Mustafi N, Grunberger A, Kohlheyer D, Bott M, Frunzke J., Metab. Eng. 14(4), 2012
PMID: 22583745
Urease of Corynebacterium glutamicum: organization of corresponding genes and investigation of activity.
Nolden L, Beckers G, Mockel B, Pfefferle W, Nampoothiri KM, Kramera R, Burkovskia A., FEMS Microbiol. Lett. 189(2), 2000
PMID: 10930756
Thermal and solvent stress cross-tolerance conferred to Corynebacterium glutamicum by adaptive laboratory evolution.
Oide S, Gunji W, Moteki Y, Yamamoto S, Suda M, Jojima T, Yukawa H, Inui M., Appl. Environ. Microbiol. 81(7), 2015
PMID: 25595768
Extensive exometabolome analysis reveals extended overflow metabolism in various microorganisms.
Paczia N, Nilgen A, Lehmann T, Gatgens J, Wiechert W, Noack S., Microb. Cell Fact. 11(), 2012
PMID: 22963408
CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands.
Pauling J, Rottger R, Tauch A, Azevedo V, Baumbach J., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22080556
Pyruvate carboxylase from Corynebacterium glutamicum: characterization, expression and inactivation of the pyc gene.
Peters-Wendisch PG, Kreutzer C, Kalinowski J, Patek M, Sahm H, Eikmanns BJ., Microbiology (Reading, Engl.) 144 ( Pt 4)(), 1998
PMID: 9579065
Adaptive laboratory evolution--harnessing the power of biology for metabolic engineering.
Portnoy VA, Bezdan D, Zengler K., Curr. Opin. Biotechnol. 22(4), 2011
PMID: 21497080
Evolution-guided optimization of biosynthetic pathways
Raman, PNAS 111(), 2014
Improving carotenoids production in yeast via adaptive laboratory evolution.
Reyes LH, Gomez JM, Kao KC., Metab. Eng. 21(), 2013
PMID: 24262517

Sambrook, 2001
Evolution of Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations.
Sandberg TE, Pedersen M, LaCroix RA, Ebrahim A, Bonde M, Herrgard MJ, Palsson BO, Sommer M, Feist AM., Mol. Biol. Evol. 31(10), 2014
PMID: 25015645
Melanin-based high-throughput screen for L-tyrosine production in Escherichia coli.
Santos CN, Stephanopoulos G., Appl. Environ. Microbiol. 74(4), 2007
PMID: 18156325
Looking for the pick of the bunch: high-throughput screening of producing microorganisms with biosensors.
Schallmey M, Frunzke J, Eggeling L, Marienhagen J., Curr. Opin. Biotechnol. 26(), 2014
PMID: 24480185
Novel biosensors based on flavonoid-responsive transcriptional regulators introduced into Escherichia coli.
Siedler S, Stahlhut SG, Malla S, Maury J, Neves AR., Metab. Eng. 21(), 2013
PMID: 24188962
Performance characteristics for sensors and circuits used to program E.coli
Tabor, 2009
The molecular diversity of adaptive convergence.
Tenaillon O, Rodriguez-Verdugo A, Gaut RL, McDonald P, Bennett AF, Long AD, Gaut BS., Science 335(6067), 2012
PMID: 22282810
The crystal structures of apo and cAMP-bound GlxR from Corynebacterium glutamicum reveal structural and dynamic changes upon cAMP binding in CRP/FNR family transcription factors.
Townsend PD, Jungwirth B, Pojer F, Bußmann M, Money VA, Cole ST, Puhler A, Tauch A, Bott M, Cann MJ, Pohl E., PLoS ONE 9(12), 2014
PMID: 25469635

AUTHOR UNKNOWN, 0

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 26453945
PubMed | Europe PMC

Suchen in

Google Scholar