Targeted genome editing in the rare actinomycete Actinoplanes sp SE50/110 by using the CRISPR/Cas9 System

Wolf T, Gren T, Thieme E, Wibberg D, Zemke T, Pühler A, Kalinowski J (2016)
Journal of Biotechnology 231: 122-128.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Abstract / Bemerkung
The application of genome editing technologies, like CRISPR/Cas9 for industrially relevant microorganisms, is becoming increasingly important. Compared to other methods of genetic engineering the decisive factor is that CRISPR/Cas9 is relatively easy to apply and thus time and effort can be significantly reduced in organisms, which are otherwise genetically difficult to access. Because of its many advantages and opportunities, we adopted the CRISPR/Cas9 technology for Actinoplanes sp. SE50/110, the producer of the diabetes type II drug acarbose. The functionality of genome editing was successfully shown by the starless and antibiotic marker-free deletion of the gene encoding the tyrosinase Me1C, which catalyzes the formation of the dark pigment eumelanin in the wild type strain. The generated AmelC2 mutant of Actinoplanes sp. SE50/110 no longer produces this pigment and therefore the supernatant does not darken. Furthermore, it was shown that the plasmid containing the gene for the Cas9 protein was removed by increasing the temperature due to its temperature-sensitive replication. The precision of the intended mutation was proven and possible off-target effects caused by the genome editing system were ruled out by genome sequencing of several mutants. (C) 2016 Elsevier B.V. All rights reserved.
Stichworte
Genome editing; Genome engineering; CRISPR/Cas9; Actinomycetes; Actinoplanes; Tyrosinase
Erscheinungsjahr
2016
Zeitschriftentitel
Journal of Biotechnology
Band
231
Seite(n)
122-128
ISSN
0168-1656
eISSN
1873-4863
Page URI
https://pub.uni-bielefeld.de/record/2905505

Zitieren

Wolf T, Gren T, Thieme E, et al. Targeted genome editing in the rare actinomycete Actinoplanes sp SE50/110 by using the CRISPR/Cas9 System. Journal of Biotechnology. 2016;231:122-128.
Wolf, T., Gren, T., Thieme, E., Wibberg, D., Zemke, T., Pühler, A., & Kalinowski, J. (2016). Targeted genome editing in the rare actinomycete Actinoplanes sp SE50/110 by using the CRISPR/Cas9 System. Journal of Biotechnology, 231, 122-128. doi:10.1016/j.jbiotec.2016.05.039
Wolf, Timo, Gren, Tetiana, Thieme, Eric, Wibberg, Daniel, Zemke, Till, Pühler, Alfred, and Kalinowski, Jörn. 2016. “Targeted genome editing in the rare actinomycete Actinoplanes sp SE50/110 by using the CRISPR/Cas9 System”. Journal of Biotechnology 231: 122-128.
Wolf, T., Gren, T., Thieme, E., Wibberg, D., Zemke, T., Pühler, A., and Kalinowski, J. (2016). Targeted genome editing in the rare actinomycete Actinoplanes sp SE50/110 by using the CRISPR/Cas9 System. Journal of Biotechnology 231, 122-128.
Wolf, T., et al., 2016. Targeted genome editing in the rare actinomycete Actinoplanes sp SE50/110 by using the CRISPR/Cas9 System. Journal of Biotechnology, 231, p 122-128.
T. Wolf, et al., “Targeted genome editing in the rare actinomycete Actinoplanes sp SE50/110 by using the CRISPR/Cas9 System”, Journal of Biotechnology, vol. 231, 2016, pp. 122-128.
Wolf, T., Gren, T., Thieme, E., Wibberg, D., Zemke, T., Pühler, A., Kalinowski, J.: Targeted genome editing in the rare actinomycete Actinoplanes sp SE50/110 by using the CRISPR/Cas9 System. Journal of Biotechnology. 231, 122-128 (2016).
Wolf, Timo, Gren, Tetiana, Thieme, Eric, Wibberg, Daniel, Zemke, Till, Pühler, Alfred, and Kalinowski, Jörn. “Targeted genome editing in the rare actinomycete Actinoplanes sp SE50/110 by using the CRISPR/Cas9 System”. Journal of Biotechnology 231 (2016): 122-128.

11 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Comparative functional genomics of the acarbose producers reveals potential targets for metabolic engineering.
Xie H, Zhao Q, Zhang X, Kang Q, Bai L., Synth Syst Biotechnol 4(1), 2019
PMID: 30723817
Integrating vectors for genetic studies in the rare Actinomycete Amycolatopsis marina.
Gao H, Murugesan B, Hoßbach J, Evans SK, Stark WM, Smith MCM., BMC Biotechnol 19(1), 2019
PMID: 31164159
Evaluation of vector systems and promoters for overexpression of the acarbose biosynthesis gene acbC in Actinoplanes sp. SE50/110.
Schaffert L, März C, Burkhardt L, Droste J, Brandt D, Busche T, Rosen W, Schneiker-Bekel S, Persicke M, Pühler A, Kalinowski J., Microb Cell Fact 18(1), 2019
PMID: 31253141
Toward Systems Metabolic Engineering of Streptomycetes for Secondary Metabolites Production.
Robertsen HL, Weber T, Kim HU, Lee SY., Biotechnol J 13(1), 2018
PMID: 29076639
Targeted Nucleotide Editing Technologies for Microbial Metabolic Engineering.
Arazoe T, Kondo A, Nishida K., Biotechnol J 13(9), 2018
PMID: 29862665
Genome improvement of the acarbose producer Actinoplanes sp. SE50/110 and annotation refinement based on RNA-seq analysis.
Wolf T, Schneiker-Bekel S, Neshat A, Ortseifen V, Wibberg D, Zemke T, Pühler A, Kalinowski J., J Biotechnol 251(), 2017
PMID: 28427920
Virgisporangium myanmarense sp. nov., a novel motile actinomycete isolated from an anthill soil in Myanmar.
Yamamura H, Miyazaki S, Ikoma K, Nakagawa Y, Hamada M, Otoguro M, Tamura T, Ando K, Phay N, Hayakawa M., J Antibiot (Tokyo) 70(10), 2017
PMID: 28698675
The MalR type regulator AcrC is a transcriptional repressor of acarbose biosynthetic genes in Actinoplanes sp. SE50/110.
Wolf T, Droste J, Gren T, Ortseifen V, Schneiker-Bekel S, Zemke T, Pühler A, Kalinowski J., BMC Genomics 18(1), 2017
PMID: 28743243

56 References

Daten bereitgestellt von Europe PubMed Central.

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694

Andrews, 2010
Strain improvement in actinomycetes in the postgenomic era.
Baltz RH., J. Ind. Microbiol. Biotechnol. 38(6), 2011
PMID: 21253811
Genetic manipulation of secondary metabolite biosynthesis for improved production in streptomyces and other actinomycetes
Baltz, J. Ind. Microbiol. Biotechnol. (), 2015
Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system.
Bassett AR, Tibbit C, Ponting CP, Liu JL., Cell Rep 4(1), 2013
PMID: 23827738
Pharmacology of alpha-glucosidase inhibition.
Bischoff H., Eur. J. Clin. Invest. 24 Suppl 3(), 1994
PMID: 8001624
Trimmomatic: a flexible trimmer for Illumina sequence data.
Bolger AM, Lohse M, Usadel B., Bioinformatics 30(15), 2014
PMID: 24695404
Ramoplanin (A-16686), a new glycolipodepsipeptide antibiotic. III. Structure elucidation.
Ciabatti R, Kettenring JK, Winters G, Tuan G, Zerilli L, Cavalleri B., J. Antibiot. 42(2), 1989
PMID: 2597278
Bacterial tyrosinases.
Claus H, Decker H., Syst. Appl. Microbiol. 29(1), 2005
PMID: 16423650
Multiplex genome engineering using CRISPR/Cas systems.
Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F., Science 339(6121), 2013
PMID: 23287718

AUTHOR UNKNOWN, 0
Actaplanin, new glycopeptide antibiotics produced by Actinoplanes missouriensis. The isolation and preliminary chemical characterization of actaplanin.
Debono M, Merkel KE, Molloy RM, Barnhart M, Presti E, Hunt AH, Hamill RL., J. Antibiot. 37(2), 1984
PMID: 6706856
CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III.
Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E., Nature 471(7340), 2011
PMID: 21455174
Phage response to CRISPR-encoded resistance in Streptococcus thermophilus.
Deveau H, Barrangou R, Garneau JE, Labonte J, Fremaux C, Boyaval P, Romero DA, Horvath P, Moineau S., J. Bacteriol. 190(4), 2007
PMID: 18065545
Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems.
DiCarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM., Nucleic Acids Res. 41(7), 2013
PMID: 23460208
A one pot, one step, precision cloning method with high throughput capability.
Engler C, Kandzia R, Marillonnet S., PLoS ONE 3(11), 2008
PMID: 18985154
Bacterial tyrosinases: old enzymes with new relevance to biotechnology.
Fairhead M, Thony-Meyer L., N Biotechnol 29(2), 2011
PMID: 21664502
Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria.
Gasiunas G, Barrangou R, Horvath P, Siksnys V., Proc. Natl. Acad. Sci. U.S.A. 109(39), 2012
PMID: 22949671
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
Genetic engineering in Actinoplanes sp. SE50/110 - development of anintergeneric conjugation system for the introduction of actinophage-basedintegrative vectors
Gren, J. Biotechnol. (), 2016
ReadXplorer--visualization and analysis of mapped sequences.
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A., Bioinformatics 30(16), 2014
PMID: 24790157
DNA targeting specificity of RNA-guided Cas9 nucleases.
Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradick TJ, Marraffini LA, Bao G, Zhang F., Nat. Biotechnol. 31(9), 2013
PMID: 23873081
One-step high-efficiency CRISPR/Cas9-mediated genome editing in Streptomyces.
Huang H, Zheng G, Jiang W, Hu H, Lu Y., Acta Biochim. Biophys. Sin. (Shanghai) 47(4), 2015
PMID: 25739462
Efficient genome editing in zebrafish using a CRISPR-Cas system.
Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh JR, Joung JK., Nat. Biotechnol. 31(3), 2013
PMID: 23360964
RNA-guided editing of bacterial genomes using CRISPR-Cas systems.
Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA., Nat. Biotechnol. 31(3), 2013
PMID: 23360965
A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.
Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E., Science 337(6096), 2012
PMID: 22745249

Kieser, 2000
Harnessing natural product assembly lines: structure, promiscuity, and engineering
Ladner, J. Ind. Microbiol. Biotechnol. (), 2015
Fast gapped-read alignment with Bowtie 2.
Langmead B, Salzberg SL., Nat. Methods 9(4), 2012
PMID: 22388286
Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9.
Li JF, Norville JE, Aach J, McCormack M, Zhang D, Bush J, Church GM, Sheen J., Nat. Biotechnol. 31(8), 2013
PMID: 23929339
Current and future prospects for CRISPR-based tools in bacteria
Luo, Biotechnol. Bioeng. (), 2015
RNA-guided human genome engineering via Cas9.
Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM., Science 339(6121), 2013
PMID: 23287722
A vector system with temperature-sensitive replication for gene disruption and mutational cloning in streptomycetes
Muth, Mol. Gen. Genet. 219(3), 1989
The contribution of melanin to microbial pathogenesis.
Nosanchuk JD, Casadevall A., Cell. Microbiol. 5(4), 2003
PMID: 12675679
Search and discovery of new antibiotics
Okami, 1988
Bacterial CRISPR: accomplishments and prospects.
Peters JM, Silvis MR, Zhao D, Hawkins JS, Gross CA, Qi LS., Curr. Opin. Microbiol. 27(), 2015
PMID: 26363124
The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110.
Schwientek P, Szczepanowski R, Ruckert C, Kalinowski J, Klein A, Selber K, Wehmeier UF, Stoye J, Puhler A., BMC Genomics 13(), 2012
PMID: 22443545
Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media
Schwientek, J. Biotechnol. (), 2012
Harnessing CRISPR-Cas systems for bacterial genome editing.
Selle K, Barrangou R., Trends Microbiol. 23(4), 2015
PMID: 25698413
Targeted genome modification of crop plants using a CRISPR-Cas system.
Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, Zhang K, Liu J, Xi JJ, Qiu JL, Gao C., Nat. Biotechnol. 31(8), 2013
PMID: 23929338
THE "TYROSINASE REACTION" OF THE ACTINOMYCETES.
Skinner CE., J. Bacteriol. 35(4), 1938
PMID: 16560113
DNA interrogation by the CRISPR RNA-guided endonuclease Cas9.
Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA., Nature 507(7490), 2014
PMID: 24476820
CRISPR-Cas9 Based Engineering of Actinomycetal Genomes.
Tong Y, Charusanti P, Zhang L, Weber T, Lee SY., ACS Synth Biol 4(9), 2015
PMID: 25806970
Chemistry and biochemistry of microbialα-glucosidase inhibitors
Truscheit, Angew. Chem. Int. Ed. Engl. 20(9), 1981
Actinoplanes
Vobis, 2012
The genus Actinoplanes and related genera
Vobis, 2006
One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering.
Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R., Cell 153(4), 2013
PMID: 23643243
Metabolic engineering of antibiotic factories: new tools for antibiotic production in actinomycetes.
Weber T, Charusanti P, Musiol-Kroll EM, Jiang X, Tong Y, Kim HU, Lee SY., Trends Biotechnol. 33(1), 2014
PMID: 25497361
Biotechnology and molecular biology of the alpha-glucosidase inhibitor acarbose.
Wehmeier UF, Piepersberg W., Appl. Microbiol. Biotechnol. 63(6), 2003
PMID: 14669056
The cytosolic and extracellular proteomes of Actinoplanes sp. SE50/110 led to the identification of gene products involved in acarbose metabolism
Wendler, J. Biotechnol. (), 2012
Carbon source dependent biosynthesis of acarviose metabolites in Actinoplanes sp. SE50/110.
Wendler S, Ortseifen V, Persicke M, Klein A, Neshat A, Niehaus K, Schneiker-Bekel S, Walter F, Wehmeier UF, Kalinowski J, Puhler A., J. Biotechnol. 191(), 2014
PMID: 25169663
Comparative proteome analysis of Actinoplanes sp. SE50/110 grown with maltose or glucose shows minor differences for acarbose biosynthesis proteins but major differences for saccharide transporters
Wendler, J. Proteomics (), 2015
Comprehensive proteome analysis of Actinoplanes sp. SE50/110 highlighting the location of proteins encoded by the acarbose and the pyochelin biosynthesis gene cluster.
Wendler S, Otto A, Ortseifen V, Bonn F, Neshat A, Schneiker-Bekel S, Walter F, Wolf T, Zemke T, Wehmeier UF, Hecker M, Kalinowski J, Becher D, Puhler A., J Proteomics 125(), 2015
PMID: 25896738
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