Construction of a prophage-free variant of Corynebacterium glutamicum ATCC 13032 - a platform strain for basic research and industrial biotechnology

Baumgart M, Unthan S, Rückert C, Sivalingam J, Grünberger A, Kalinowski J, Bott M, Noack S, Frunzke J (2013)
Applied and environmental microbiology 79(19): 6006-6015.

Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Autor
; ; ; ; ; ; ; ;
Abstract / Bemerkung
: The activity of bacteriophages and phage-related mobile elements is a major source for genome rearrangements and genetic instability of their bacterial hosts. The genome of the industrial amino acid producer Corynebacterium glutamicum ATCC 13032 contains three prophages (CGP1-3) of so far unknown functionality. Several phage genes are regularly expressed and the large prophage CGP3 (∼190 kbp) has recently been shown to be induced under certain stress conditions. Here, we present the construction of MB001, a prophage-free variant of C. glutamicum ATCC 13032 with a 6 % reduced genome. This strain does not show any unfavorable properties during extensive phenotypic characterization under various standard and stress conditions. As expected, we observed an improved growth and fitness of MB001 under SOS-response inducing conditions that trigger CGP3 induction in the wild type strain. Further studies revealed that MB001 has a significantly increased transformation efficiency and produced about 30 % more of the heterologous model protein eYFP, presumably as a consequence of an increased plasmid copy number. These effects were attributed to the loss of the restriction-modification system (cg1996-98) located within CGP3. The deletion of the prophages without any negative effect results in a novel platform strain for metabolic engineering and represents a useful step towards the construction of a C. glutamicum chassis genome of strain ATCC 13032 for biotechnological applications and synthetic biology.
Erscheinungsjahr
Zeitschriftentitel
Applied and environmental microbiology
Band
79
Ausgabe
19
Seite(n)
6006-6015
ISSN
PUB-ID

Zitieren

Baumgart M, Unthan S, Rückert C, et al. Construction of a prophage-free variant of Corynebacterium glutamicum ATCC 13032 - a platform strain for basic research and industrial biotechnology. Applied and environmental microbiology. 2013;79(19):6006-6015.
Baumgart, M., Unthan, S., Rückert, C., Sivalingam, J., Grünberger, A., Kalinowski, J., Bott, M., et al. (2013). Construction of a prophage-free variant of Corynebacterium glutamicum ATCC 13032 - a platform strain for basic research and industrial biotechnology. Applied and environmental microbiology, 79(19), 6006-6015. doi:10.1128/AEM.01634-13
Baumgart, M., Unthan, S., Rückert, C., Sivalingam, J., Grünberger, A., Kalinowski, J., Bott, M., Noack, S., and Frunzke, J. (2013). Construction of a prophage-free variant of Corynebacterium glutamicum ATCC 13032 - a platform strain for basic research and industrial biotechnology. Applied and environmental microbiology 79, 6006-6015.
Baumgart, M., et al., 2013. Construction of a prophage-free variant of Corynebacterium glutamicum ATCC 13032 - a platform strain for basic research and industrial biotechnology. Applied and environmental microbiology, 79(19), p 6006-6015.
M. Baumgart, et al., “Construction of a prophage-free variant of Corynebacterium glutamicum ATCC 13032 - a platform strain for basic research and industrial biotechnology”, Applied and environmental microbiology, vol. 79, 2013, pp. 6006-6015.
Baumgart, M., Unthan, S., Rückert, C., Sivalingam, J., Grünberger, A., Kalinowski, J., Bott, M., Noack, S., Frunzke, J.: Construction of a prophage-free variant of Corynebacterium glutamicum ATCC 13032 - a platform strain for basic research and industrial biotechnology. Applied and environmental microbiology. 79, 6006-6015 (2013).
Baumgart, Meike, Unthan, Simon, Rückert, Christian, Sivalingam, Jasintha, Grünberger, Alexander, Kalinowski, Jörn, Bott, Michael, Noack, Stephan, and Frunzke, Julia. “Construction of a prophage-free variant of Corynebacterium glutamicum ATCC 13032 - a platform strain for basic research and industrial biotechnology”. Applied and environmental microbiology 79.19 (2013): 6006-6015.

52 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Mu-driven transposition of recombinant mini-Mu unit DNA in the Corynebacterium glutamicum chromosome.
Gorshkova NV, Lobanova JS, Tokmakova IL, Smirnov SV, Akhverdyan VZ, Krylov AA, Mashko SV., Appl Microbiol Biotechnol 102(6), 2018
PMID: 29392386
A RecET-assisted CRISPR-Cas9 genome editing in Corynebacterium glutamicum.
Wang B, Hu Q, Zhang Y, Shi R, Chai X, Liu Z, Shang X, Zhang Y, Wen T., Microb Cell Fact 17(1), 2018
PMID: 29685154
Functional Characterization of a Small Alarmone Hydrolase in Corynebacterium glutamicum.
Ruwe M, Rückert C, Kalinowski J, Persicke M., Front Microbiol 9(), 2018
PMID: 29867827
Phage Therapy: What Have We Learned?
Górski A, Międzybrodzki R, Łobocka M, Głowacka-Rutkowska A, Bednarek A, Borysowski J, Jończyk-Matysiak E, Łusiak-Szelachowska M, Weber-Dąbrowska B, Bagińska N, Letkiewicz S, Dąbrowska K, Scheres J., Viruses 10(6), 2018
PMID: 29843391
Transport and metabolic engineering of the cell factory Corynebacterium glutamicum.
Pérez-García F, Wendisch VF., FEMS Microbiol Lett 365(16), 2018
PMID: 29982619
BioPS: System for screening and assessment of biofuel-production potential of cyanobacteria.
Motwalli O, Essack M, Salhi A, Hanks J, Mijakovic I, Bajic VB., PLoS One 13(8), 2018
PMID: 30096176
Synthetic biology approaches to access renewable carbon source utilization in Corynebacterium glutamicum.
Zhao N, Qian L, Luo G, Zheng S., Appl Microbiol Biotechnol 102(22), 2018
PMID: 30218378
Efficient Production of the Dicarboxylic Acid Glutarate by Corynebacterium glutamicum via a Novel Synthetic Pathway.
Pérez-García F, Jorge JMP, Dreyszas A, Risse JM, Wendisch VF., Front Microbiol 9(), 2018
PMID: 30425699
Mutations in Peptidoglycan Synthesis Gene ponA Improve Electrotransformation Efficiency of Corynebacterium glutamicum ATCC 13869.
Liu J, Wang Y, Lu Y, Ni X, Guo X, Zhao J, Chen J, Dele-Osibanjo T, Zheng P, Sun J, Ma Y., Appl Environ Microbiol 84(24), 2018
PMID: 30341076
Heterologous expression of the Halothiobacillus neapolitanus carboxysomal gene cluster in Corynebacterium glutamicum.
Baumgart M, Huber I, Abdollahzadeh I, Gensch T, Frunzke J., J Biotechnol 258(), 2017
PMID: 28359868
Isoprenoid Pyrophosphate-Dependent Transcriptional Regulation of Carotenogenesis in Corynebacterium glutamicum.
Henke NA, Heider SAE, Hannibal S, Wendisch VF, Peters-Wendisch P., Front Microbiol 8(), 2017
PMID: 28484430
Production of amino acids - Genetic and metabolic engineering approaches.
Lee JH, Wendisch VF., Bioresour Technol 245(pt b), 2017
PMID: 28552565
Building a bio-based industry in the Middle East through harnessing the potential of the Red Sea biodiversity.
Nielsen J, Archer J, Essack M, Bajic VB, Gojobori T, Mijakovic I., Appl Microbiol Biotechnol 101(12), 2017
PMID: 28528426
Synthetic biology approaches for the production of plant metabolites in unicellular organisms.
Moses T, Mehrshahi P, Smith AG, Goossens A., J Exp Bot 68(15), 2017
PMID: 28449101
Efficient gene editing in Corynebacterium glutamicum using the CRISPR/Cas9 system.
Peng F, Wang X, Sun Y, Dong G, Yang Y, Liu X, Bai Z., Microb Cell Fact 16(1), 2017
PMID: 29137643
Expression of recombinant protein using Corynebacterium Glutamicum: progress, challenges and applications.
Liu X, Yang Y, Zhang W, Sun Y, Peng F, Jeffrey L, Harvey L, McNeil B, Bai Z., Crit Rev Biotechnol 36(4), 2016
PMID: 25714007
High-titer biosynthesis of hyaluronic acid by recombinant Corynebacterium glutamicum.
Cheng F, Gong Q, Yu H, Stephanopoulos G., Biotechnol J 11(4), 2016
PMID: 26709615
Updates on industrial production of amino acids using Corynebacterium glutamicum.
Wendisch VF, Jorge JMP, Pérez-García F, Sgobba E., World J Microbiol Biotechnol 32(6), 2016
PMID: 27116971
Construction of a Corynebacterium glutamicum platform strain for the production of stilbenes and (2S)-flavanones.
Kallscheuer N, Vogt M, Stenzel A, Gätgens J, Bott M, Marienhagen J., Metab Eng 38(), 2016
PMID: 27288926
Engineering Corynebacterium glutamicum for fast production of L-lysine and L-pipecolic acid.
Pérez-García F, Peters-Wendisch P, Wendisch VF., Appl Microbiol Biotechnol 100(18), 2016
PMID: 27345060
Roles of export genes cgmA and lysE for the production of L-arginine and L-citrulline by Corynebacterium glutamicum.
Lubitz D, Jorge JM, Pérez-García F, Taniguchi H, Wendisch VF., Appl Microbiol Biotechnol 100(19), 2016
PMID: 27350619
Production of the Marine Carotenoid Astaxanthin by Metabolically Engineered Corynebacterium glutamicum.
Henke NA, Heider SA, Peters-Wendisch P, Wendisch VF., Mar Drugs 14(7), 2016
PMID: 27376307
Silencing of cryptic prophages in Corynebacterium glutamicum.
Pfeifer E, Hünnefeld M, Popa O, Polen T, Kohlheyer D, Baumgart M, Frunzke J., Nucleic Acids Res 44(21), 2016
PMID: 27492287
The quest for the minimal bacterial genome.
Martínez-García E, de Lorenzo V., Curr Opin Biotechnol 42(), 2016
PMID: 27660908
Ciprofloxacin triggered glutamate production by Corynebacterium glutamicum.
Lubitz D, Wendisch VF., BMC Microbiol 16(1), 2016
PMID: 27717325
Use of a Sec signal peptide library from Bacillus subtilis for the optimization of cutinase secretion in Corynebacterium glutamicum.
Hemmerich J, Rohe P, Kleine B, Jurischka S, Wiechert W, Freudl R, Oldiges M., Microb Cell Fact 15(1), 2016
PMID: 27927208
Chassis organism from Corynebacterium glutamicum--a top-down approach to identify and delete irrelevant gene clusters.
Unthan S, Baumgart M, Radek A, Herbst M, Siebert D, Brühl N, Bartsch A, Bott M, Wiechert W, Marin K, Hans S, Krämer R, Seibold G, Frunzke J, Kalinowski J, Rückert C, Wendisch VF, Noack S., Biotechnol J 10(2), 2015
PMID: 25139579
Genome sequence of the soil bacterium Corynebacterium callunae type strain DSM 20147(T).
Persicke M, Albersmeier A, Bednarz H, Niehaus K, Kalinowski J, Rückert C., Stand Genomic Sci 10(), 2015
PMID: 26203323
Genome-based identification of active prophage regions by next generation sequencing in Bacillus licheniformis DSM13.
Hertel R, Rodríguez DP, Hollensteiner J, Dietrich S, Leimbach A, Hoppert M, Liesegang H, Volland S., PLoS One 10(3), 2015
PMID: 25811873
Live cell imaging of SOS and prophage dynamics in isogenic bacterial populations.
Helfrich S, Pfeifer E, Krämer C, Sachs CC, Wiechert W, Kohlheyer D, Nöh K, Frunzke J., Mol Microbiol 98(4), 2015
PMID: 26235130
Analysis of SOS-induced spontaneous prophage induction in Corynebacterium glutamicum at the single-cell level.
Nanda AM, Heyer A, Krämer C, Grünberger A, Kohlheyer D, Frunzke J., J Bacteriol 196(1), 2014
PMID: 24163339
Clostridium difficile phages: still difficult?
Hargreaves KR, Clokie MR., Front Microbiol 5(), 2014
PMID: 24808893
Optimization of the IPP Precursor Supply for the Production of Lycopene, Decaprenoxanthin and Astaxanthin by Corynebacterium glutamicum.
Heider SA, Wolf N, Hofemeier A, Peters-Wendisch P, Wendisch VF., Front Bioeng Biotechnol 2(), 2014
PMID: 25191655

59 References

Daten bereitgestellt von Europe PubMed Central.

Streamlining genomes: toward the generation of simplified and stabilized microbial systems.
Leprince A, van Passel MW, dos Santos VA., Curr. Opin. Biotechnol. 23(5), 2012
PMID: 22651991
Genome-scale engineering for systems and synthetic biology.
Esvelt KM, Wang HH., Mol. Syst. Biol. 9(), 2013
PMID: 23340847
Life: in search of the simplest cell.
Szathmary E., Nature 433(7025), 2005
PMID: 15690023
Studies of amino acid fermentation. I. Production of L-glutamic acid by various microorganisms
Kinoshita S, Udaka S, Shimono M., 1957

Wendisch VF., 2007
Superpositioning of deletions promotes growth of Escherichia coli with a reduced genome.
Mizoguchi H, Sawano Y, Kato J, Mori H., DNA Res. 15(5), 2008
PMID: 18753290
Bacillus minimum genome factory: effective utilization of microbial genome information.
Ara K, Ozaki K, Nakamura K, Yamane K, Sekiguchi J, Ogasawara N., Biotechnol. Appl. Biochem. 46(Pt 3), 2007
PMID: 17115975
Low-mutation-rate, reduced-genome Escherichia coli: an improved host for faithful maintenance of engineered genetic constructs.
Csorgo B, Feher T, Timar E, Blattner FR, Posfai G., Microb. Cell Fact. 11(), 2012
PMID: 22264280
Genome engineering reveals large dispensable regions in Bacillus subtilis.
Westers H, Dorenbos R, van Dijl JM, Kabel J, Flanagan T, Devine KM, Jude F, Seror SJ, Beekman AC, Darmon E, Eschevins C, de Jong A, Bron S, Kuipers OP, Albertini AM, Antelmann H, Hecker M, Zamboni N, Sauer U, Bruand C, Ehrlich DS, Alonso JC, Salas M, Quax WJ., Mol. Biol. Evol. 20(12), 2003
PMID: 12949151
Population fitness and the regulation of genes by bacterial viruses
Chen Y, Golding I, Sawai S, Guo L, Cox EC., 2005
Enhanced recombinant protein productivity by genome reduction in Bacillus subtilis.
Morimoto T, Kadoya R, Endo K, Tohata M, Sawada K, Liu S, Ozawa T, Kodama T, Kakeshita H, Kageyama Y, Manabe K, Kanaya S, Ara K, Ozaki K, Ogasawara N., DNA Res. 15(2), 2008
PMID: 18334513
Emergent properties of reduced-genome Escherichia coli.
Posfai G, Plunkett G 3rd, Feher T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, Burland V, Harcum SW, Blattner FR., Science 312(5776), 2006
PMID: 16645050
Large-scale engineering of the Corynebacterium glutamicum genome.
Suzuki N, Okayama S, Nonaka H, Tsuge Y, Inui M, Yukawa H., Appl. Environ. Microbiol. 71(6), 2005
PMID: 15933044
New multiple-deletion method for the Corynebacterium glutamicum genome, using a mutant lox sequence.
Suzuki N, Nonaka H, Tsuge Y, Inui M, Yukawa H., Appl. Environ. Microbiol. 71(12), 2005
PMID: 16332837
Prophages and bacterial genomics: what have we learned so far?
Casjens S., Mol. Microbiol. 49(2), 2003
PMID: 12886937
Bacteriophage control of bacterial virulence.
Wagner PL, Waldor MK., Infect. Immun. 70(8), 2002
PMID: 12117903
The impact of prophages on bacterial chromosomes.
Canchaya C, Fournous G, Brussow H., Mol. Microbiol. 53(1), 2004
PMID: 15225299
The diverse and dynamic structure of bacterial genomes.
Casjens S., Annu. Rev. Genet. 32(), 1998
PMID: 9928484
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
The genomes of amino acid-producing corynebacteria
Kalinowski J., 2005
Comparative analysis of the Corynebacterium glutamicum group and complete genome sequence of strain R.
Yukawa H, Omumasaba CA, Nonaka H, Kos P, Okai N, Suzuki N, Suda M, Tsuge Y, Watanabe J, Ikeda Y, Vertes AA, Inui M., Microbiology (Reading, Engl.) 153(Pt 4), 2007
PMID: 17379713
Population Heterogeneity in Corynebacterium glutamicum ATCC 13032 caused by prophage CGP3.
Frunzke J, Bramkamp M, Schweitzer JE, Bott M., J. Bacteriol. 190(14), 2008
PMID: 18487330
The DtxR regulon of Corynebacterium glutamicum.
Wennerhold J, Bott M., J. Bacteriol. 188(8), 2006
PMID: 16585752

Sambrook J, Fritsch EF, Maniatis T., 1989
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
Studies on transformation of Escherichia coli with plasmids.
Hanahan D., J. Mol. Biol. 166(4), 1983
PMID: 6345791
A disposable picolitre bioreactor for cultivation and investigation of industrially relevant bacteria on the single cell level.
Grunberger A, Paczia N, Probst C, Schendzielorz G, Eggeling L, Noack S, Wiechert W, Kohlheyer D., Lab Chip 12(11), 2012
PMID: 22511122
Efficient electrotransformation of corynebacterium diphtheriae with a mini-replicon derived from the Corynebacterium glutamicum plasmid pGA1.
Tauch A, Kirchner O, Loffler B, Gotker S, Puhler A, Kalinowski J., Curr. Microbiol. 45(5), 2002
PMID: 12232668
Lysogeny.
LWOFF A., Bacteriol Rev 17(4), 1953
PMID: 13105613
An automated workflow for enhancing microbial bioprocess optimization on a novel microbioreactor platform.
Rohe P, Venkanna D, Kleine B, Freudl R, Oldiges M., Microb. Cell Fact. 11(), 2012
PMID: 23113930
Combined effect of improved cell yield and increased specific productivity enhances recombinant enzyme production in genome-reduced Bacillus subtilis strain MGB874.
Manabe K, Kageyama Y, Morimoto T, Ozawa T, Sawada K, Endo K, Tohata M, Ara K, Ozaki K, Ogasawara N., Appl. Environ. Microbiol. 77(23), 2011
PMID: 21965396
High efficiency electroporation of intact Corynebacterium glutamicum cells.
Liebl W, Bayerl A, Schein B, Stillner U, Schleifer KH., FEMS Microbiol. Lett. 53(3), 1989
PMID: 2612892
Presence of mrr- and mcr-like restriction systems in coryneform bacteria.
Vertes AA, Inui M, Kobayashi M, Kurusu Y, Yukawa H., Res. Microbiol. 144(3), 1993
PMID: 8210675
Analysis of nucleotide methylation in DNA from Corynebacterium glutamicum and related species.
Jang KH, Chambers PJ, Britz ML., FEMS Microbiol. Lett. 136(3), 1996
PMID: 8867385
Selfish behavior of restriction-modification systems.
Naito T, Kusano K, Kobayashi I., Science 267(5199), 1995
PMID: 7846533
Characterization of a region of plasmid pBL1 of Brevibacterium lactofermentum involved in replication via the rolling circle model.
Fernandez-Gonzalez C, Cadenas RF, Noirot-Gros MF, Martin JF, Gil JA., J. Bacteriol. 176(11), 1994
PMID: 8195068
Characterization of an endogenous plasmid and development of cloning vectors and a transformation system in
Santamaria R, Gil JA, Mesas JM, Martin JF., 1984
Cryptic plasmids in glutamic acid-producing bacteria
Miwa K, Matsui H, Terabe M, Nakamori S, Sano K, Momose H., 1984
Replication and control of circular bacterial plasmids.
del Solar G, Giraldo R, Ruiz-Echevarria MJ, Espinosa M, Diaz-Orejas R., Microbiol. Mol. Biol. Rev. 62(2), 1998
PMID: 9618448
The family of highly interrelated single-stranded deoxyribonucleic acid plasmids.
Gruss A, Ehrlich SD., Microbiol. Rev. 53(2), 1989
PMID: 2666843
Plasmid copy number control: an ever-growing story.
del Solar G, Espinosa M., Mol. Microbiol. 37(3), 2000
PMID: 10931343
The nucleotide sequence of pACYC184.
Rose RE., Nucleic Acids Res. 16(1), 1988
PMID: 3340533
Destabilized eYFP variants for dynamic gene expression studies in Corynebacterium glutamicum.
Hentschel E, Will C, Mustafi N, Burkovski A, Rehm N, Frunzke J., Microb Biotechnol 6(2), 2012
PMID: 22938655

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 23892752
PubMed | Europe PMC

Suchen in

Google Scholar