RNA-guided single/double gene repressions in Corynebacterium glutamicum using an efficient CRISPR interference and its application to industrial strain

Microbial Cell Factories

Volumn 17, Issue 1, 2018, Pages

  Park, Jaehyun ^a   Shin, Hyojung ^b,c   Lee, Sun Mi ^b   Um, Youngsoon ^b   Woo, Han Min ^a  

^a Sungkyunkwan University   (South Korea)

^b Korea Institute of Science and Technology   (South Korea)

^c GyeongSangBukDo Government Public Institute of Health and Environment   (South Korea)

Author keywords

Corynebacterium glutamicum; CRISPR interference; Metabolic engineering; Synthetic biology

Indexed keywords

CITRATE SYNTHASE; LYSINE; MESSENGER RNA; GUIDE RNA;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CONTROLLED STUDY; CORYNEBACTERIUM GLUTAMICUM; GENE REPRESSION; GLGC GENE; GLTA GENE; IDSA GENE; NONHUMAN; PHENOTYPE; PYC GENE; CRISPR CAS SYSTEM; GENE EXPRESSION REGULATION; GENE SILENCING; GENE VECTOR; GENETICS; METABOLIC ENGINEERING; PHYSIOLOGY; PLASMID; PROCEDURES; SYNTHETIC BIOLOGY;

CITRATE (SI)-SYNTHASE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CORYNEBACTERIUM GLUTAMICUM; CRISPR-CAS SYSTEMS; GENE EXPRESSION REGULATION, BACTERIAL; GENE SILENCING; GENETIC VECTORS; METABOLIC ENGINEERING; PLASMIDS; RNA, GUIDE; SYNTHETIC BIOLOGY;

EID: 85040323809     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/s12934-017-0843-1     Document Type: Article

References (27)

1. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013;152:1173-83.
2. Yao L, Cengic I, Anfelt J, Hudson EP. Multiple gene repression in Cyanobacteria using CRISPRi. ACS Synth Biol. 2016;5:207-12.
3. Choudhary E, Thakur P, Pareek M, Agarwal N. Gene silencing by CRISPR interference in mycobacteria. Nat Commun. 2015;6:6267.
4. Smith JD, Suresh S, Schlecht U, Wu M, Wagih O, Peltz G, Davis RW, Steinmetz LM, Parts L, St Onge RP. Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design. Genome Biol. 2016;17:45.
5. Westbrook AW, Moo-Young M, Chou CP, Kivisaar M. Development of a CRISPR-Cas9 tool kit for comprehensive engineering of Bacillus subtilis. Appl Environ Microbiol. 2016;82:4876-95.
6. Lv L, Ren YL, Chen JC, Wu Q, Chen GQ. Application of CRISPRi for prokaryotic metabolic engineering involving multiple genes, a case study: controllable P(3HB-co-4HB) biosynthesis. Metab Eng. 2015;29:160-8.
7. Kim SK, Han GH, Seong W, Kim H, Kim SW, Lee DH, Lee SG. CRISPR interference-guided balancing of a biosynthetic mevalonate pathway increases terpenoid production. Metab Eng. 2016;38:228-40.
8. Eggeling L, Bott M. A giant market and a powerful metabolism: l-lysine provided by Corynebacterium glutamicum. Appl Microbiol Biotechnol. 2015;99:3387-94.
9. Cleto S, Jensen JV, Wendisch VF, Lu TK. Corynebacterium glutamicum metabolic engineering with CRISPR interference (CRISPRi). ACS Synth Biol. 2016;5:375-85.
10. Zhang B, Liu ZQ, Liu C, Zheng YG. Application of CRISPRi in Corynebacterium glutamicum for shikimic acid production. Biotechnol Lett. 2016;38:2153-61.
11. Kang MK, Lee J, Um Y, Lee TS, Bott M, Park SJ, Woo HM. Synthetic biology platform of CoryneBrick vectors for gene expression in Corynebacterium glutamicum and its application to xylose utilization. Appl Microbiol Biotechnol. 2014;98:5991-6002.
12. Larson MH, Gilbert LA, Wang X, Lim WA, Weissman JS, Qi LS. CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nat Protoc. 2013;8:2180-96.
13. Bae S, Park J, Kim JS. Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics. 2014;30:1473-5.
14. Peters-Wendisch PG, Kreutzer C, Kalinowski J, Patek M, Sahm H, Eikmanns BJ. Pyruvate carboxylase from Corynebacterium glutamicum: characterization, expression and inactivation of the pyc gene. Microbiology. 1998;144(Pt 4):915-27.
15. van Ooyen J, Noack S, Bott M, Reth A, Eggeling L. Improved l-lysine production with Corynebacterium glutamicum and systemic insight into citrate synthase flux and activity. Biotechnol Bioeng. 2012;109:2070-81.
16. Wendisch VF, de Graaf AA, Sahm H, Eikmanns BJ. Quantitative determination of metabolic fluxes during coutilization of two carbon sources: comparative analyses with Corynebacterium glutamicum during growth on acetate and/or glucose. J Bacteriol. 2000;182:3088-96.
17. Seibold G, Dempf S, Schreiner J, Eikmanns BJ. Glycogen formation in Corynebacterium glutamicum and role of ADP-glucose pyrophosphorylase. Microbiology. 2007;153:1275-85.
18. Heider SA, Peters-Wendisch P, Beekwilder J, Wendisch VF. IdsA is the major geranylgeranyl pyrophosphate synthase involved in carotenogenesis in Corynebacterium glutamicum. FEBS J. 2014;281:4906-20.
19. Eggeling L, Bott M. Handbook of Corynebacterium glutamicum. Boca Raton: CRC Press; 2010.
20. Choo S, Um Y, Han SO, Woo HM. Engineering of Corynebacterium glutamicum to utilize methyl acetate, a potential feedstock derived by carbonylation of methanol with CO. J Biotechnol. 2016;224:47-50.
21. Kabus A, Niebisch A, Bott M. Role of cytochrome bd oxidase from Corynebacterium glutamicum in growth and lysine production. Appl Environ Microbiol. 2007;73:861-8.
22. Kim EM, Um Y, Bott M, Woo HM. Engineering of Corynebacterium glutamicum for growth and succinate production from levoglucosan, a pyrolytic sugar substrate. FEMS Microbiol Lett. 2015;362:fnv161.
23. Larisch C, Nakunst D, Huser AT, Tauch A, Kalinowski J. The alternative sigma factor SigB of Corynebacterium glutamicum modulates global gene expression during transition from exponential growth to stationary phase. BMC Genomics. 2007;8:4.
24. -Ct method. Methods. 2001;25:402-8.
25. Eikmanns BJ, Thum-Schmitz N, Eggeling L, Ludtke KU, Sahm H. Nucleotide sequence, expression and transcriptional analysis of the Corynebacterium glutamicum gltA gene encoding citrate synthase. Microbiology. 1994;140(Pt 8):1817-28.
26. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J Mol Biol. 1983;166:557-80.
27. Dusch N, Pühler A, Kalinowski J. Expression of the Corynebacterium glutamicum panD gene encoding l-aspartate-alpha-decarboxylase leads to pantothenate overproduction in Escherichia coli. Appl Environ Microbiol. 1999;65:1530-9.