Multiple Gene Repression in Cyanobacteria Using CRISPRi

ACS Synthetic Biology

Volumn 5, Issue 3, 2016, Pages 207-212

  Yao, Lun ^a   Cengic, Ivana ^a   Anfelt, Josefine ^a   Hudson, Elton P ^a  

^a ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ALDEHYDE REDUCTASE; GLYCOGEN; GREEN FLUORESCENT PROTEIN; NITROGEN; OXIDOREDUCTASE; ALDEHYDE DEHYDROGENASE; BACTERIAL PROTEIN;

ARTICLE; CARBON STORAGE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CYANOBACTERIUM; GENE REPRESSION; METABOLIC ENGINEERING; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; STREPTROCOCCUS PYOGENES; SYNECHOCYSTIS; SYNTHETIC BIOLOGY; CRISPR CAS SYSTEM; DOWN REGULATION; FLOW CYTOMETRY; GENETICS; METABOLISM; WESTERN BLOTTING;

ALDEHYDE DEHYDROGENASE; ALDEHYDE REDUCTASE; BACTERIAL PROTEINS; BLOTTING, WESTERN; CRISPR-CAS SYSTEMS; CYANOBACTERIA; DOWN-REGULATION; FLOW CYTOMETRY; GREEN FLUORESCENT PROTEINS;

EID: 84961794371     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/acssynbio.5b00264     Document Type: Article

References (38)

1. Hsu, P. D., Lander, E. S., and Zhang, F. (2014) Development and Applications of CRISPR-Cas9 for Genome Engineering Cell 157, 1262-1278 10.1016/j.cell.2014.05.010
2. Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., and Charpentier, E. (2012) A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity Science 337, 816-822 10.1126/science.1225829
3. Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., and Lim, W. A. (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression Cell 152, 1173-83 10.1016/j.cell.2013.02.022
4. Bikard, D., Jiang, W., Samai, P., Hochschild, A., Zhang, F., and Marraffini, L. a. (2013) Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system Nucleic Acids Res. 41, 7429-37 10.1093/nar/gkt520
5. Stovicek, V., Borodina, I., and Forster, J. (2015) CRISPR-Cas system enables fast and simple genome editing of industrial Saccharomyces cerevisiae strains Metab. Eng. Commun. 2, 13-22 10.1016/j.meteno.2015.03.001
6. Zalatan, J. G., Lee, M. E., Almeida, R., Gilbert, L. a., Whitehead, E. H., La Russa, M., Tsai, J. C., Weissman, J. S., Dueber, J. E., Qi, L. S., and Lim, W. a. (2014) Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds Cell 160, 339-350 10.1016/j.cell.2014.11.052
7. Lv, L., Ren, Y., Chen, J., Wu, Q., and Chen, G. (2015) Application of CRISPRi for prokaryotic metabolic engineering involving multiple genes, a case study: Controllable P (3HB- co -4HB) biosynthesis Metab. Eng. 29, 1-9 10.1016/j.ymben.2015.03.013
8. Scholz, I., Lange, S. J., Hein, S., Hess, W. R., and Backofen, R. (2013) CRISPR-Cas systems in the cyanobacterium Synechocystis sp. PCC6803 exhibit distinct processing pathways involving at least two Cas6 and a Cmr2 protein PLoS One 8, e56470 10.1371/journal.pone.0056470
9. Hein, S., Scholz, I., Voß, B., and Hess, W. R. (2013) Adaptation and modification of three CRISPR loci in two closely related cyanobacteria RNA Biol. 10, 852-64 10.4161/rna.24160
10. Anfelt, J., Kaczmarzyk, D., Shabestary, K., Renberg, B., Uhlen, M., Nielsen, J., and Hudson, E. P. (2015) Genetic and nutrient modulation of acetyl-CoA levels in Synechocystis for n-butanol production Microb. Cell Fact. 14, 1-12 10.1186/s12934-015-0355-9
11. Oliver, J. W. K. and Atsumi, S. (2014) Metabolic design for cyanobacterial chemical synthesis Photosynth. Res. 120, 249-61 10.1007/s11120-014-9997-4
12. Baroukh, C., Muñoz-Tamayo, R., Steyer, J.-P., and Bernard, O. (2015) A state of the art of metabolic networks of unicellular microalgae and cyanobacteria for biofuel production Metab. Eng. 30, 49-60 10.1016/j.ymben.2015.03.019
13. Hammar, P., Angermayr, S., Sjöström, S., van der Meer, J., Hellingwerf, K., Hudson, E. P., and Jönsson, H. (2015) Single cell screening of photosynthetic growth and lactate production by cyanobacteria Biotechnol. Biofuels 8, 1-8 10.1186/s13068-015-0380-2
14. Griese, M., Lange, C., and Soppa, J. (2011) Ploidy in cyanobacteria FEMS Microbiol. Lett. 323, 124-131 10.1111/j.1574-6968.2011.02368.x
15. Begemann, M. B., Zess, E. K., Walters, E. M., Schmitt, E. F., Markley, A. L., and Pfleger, B. F. (2013) An Organic Acid Based Counter Selection System for Cyanobacteria PLoS One 8, 1-12 10.1371/journal.pone.0076594
16. Cheah, Y. E., Albers, S. C., and Peebles, C. a M. (2013) A novel counter-selection method for markerless genetic modification in Synechocystis sp. PCC 6803 Biotechnol. Prog. 29, 23-30 10.1002/btpr.1661
17. Zess, E. K., Begemann, M. B., and Pfleger, B. F. (2015) Construction of new synthetic biology tools for the control of gene expression in the cyanobacterium Synechococcus sp. strain PCC 7002 Biotechnol. Bioeng. 10.1002/bit.25713
18. Ramey, C. J., Barón-Sola, á., Aucoin, H. R., and Boyle, N. R. (2015) Genome engineering in cyanobacteria: where we are and where we need to go ACS Synth. Biol. 4, 1186-1196 10.1021/acssynbio.5b00043
19. Larson, M. H., Gilbert, L. A., Wang, X., Lim, W. A., Weissman, J. S., and Qi, L. S. (2013) CRISPR interference (CRISPRi) for sequence-specific control of gene expression Nat. Protoc. 8, 2180-2196 10.1038/nprot.2013.132
20. Xiao, A., Cheng, Z., Kong, L., Zhu, Z., Lin, S., Gao, G., and Zhang, B. (2014) CasOT: a genome-wide Cas9/gRNA off-target searching tool Bioinformatics 30, 1180-1182 10.1093/bioinformatics/btt764
21. Agrawal, G. K., Kato, H., Asayama, M., and Shirai, M. (2001) An AU-box motif upstream of the SD sequence of light-dependent psbA transcripts confers mRNA instability in darkness in cyanobacteria Nucleic Acids Res. 29, 1835-1843 10.1093/nar/29.9.1835
22. Huang, H.-H. and Lindblad, P. (2013) Wide-dynamic-range promoters engineered for cyanobacteria J. Biol. Eng. 7, 10 10.1186/1754-1611-7-10
23. Kusakabe, T., Tatsuke, T., Tsuruno, K., Hirokawa, Y., Atsumi, S., Liao, J. C., and Hanai, T. (2013) Engineering a synthetic pathway in cyanobacteria for isopropanol production directly from carbon dioxide and light Metab. Eng. 20, 101-8 10.1016/j.ymben.2013.09.007
24. Hein, S., Tran, H., and Steinbüchel, A. (1998) Synechocystis sp. PCC6803 possesses a two-component polyhydroxyalkanoic acid synthase similar to that of anoxygenic purple sulfur bacteria Arch. Microbiol. 170, 162-170 10.1007/s002030050629
25. Sauer, J., Schreiber, U., Schmid, R., Völker, U., and Forchhammer, K. (2001) Nitrogen starvation-induced chlorosis in Synechococcus PCC 7942. Low-level photosynthesis as a mechanism of long-term survival Plant Physiol. 126, 233-243 10.1104/pp.126.1.233
26. Gründel, M., Scheunemann, R., Lockau, W., and Zilliges, Y. (2012) Impaired glycogen synthesis causes metabolic overflow reactions and affects stress responses in the cyanobacterium Synechocystis sp. PCC 6803 Microbiology 158, 3032-43 10.1099/mic.0.062950-0
27. Schirmer, A., Rude, M., Li, X., Popova, E., and Del Cardayre, S. (2010) Microbial Biosynthesis of Alkanes Science (Washington, DC, U. S.) 329, 559-562 10.1126/science.1187936
28. Rodriguez, G. M. and Atsumi, S. (2014) Toward aldehyde and alkane production by removing aldehyde reductase activity in Escherichia coli Metab. Eng. 25, 227-237 10.1016/j.ymben.2014.07.012
29. Hintzpeter, J., Martin, H.-J., and Maser, E. (2015) Reduction of lipid peroxidation products and advanced glycation end-product precursors by cyanobacterial aldo-keto reductase AKR3G1 - a founding member of the AKR3G subfamily FASEB J. 29, 263-273 10.1096/fj.14-258327
30. Kanesaki, Y., Yamamoto, H., Paithoonrangsarid, K., Shoumskaya, M., Suzuki, I., Hayashi, H., and Murata, N. (2007) Histidine kinases play important roles in the perception and signal transduction of hydrogen peroxide in the cyanobacterium, Synechocystis sp. PCC 6803 Plant J. 49, 313-24 10.1111/j.1365-313X.2006.02959.x
31. Gao, Z., Zhao, H., Li, Z., Tan, X., and Lu, X. (2012) Photosynthetic production of ethanol from carbon dioxide in genetically engineered cyanobacteria Energy Environ. Sci. 5, 9857 10.1039/c2ee22675h
32. Vidal, R., López-Maury, L., Guerrero, M. G., and Florencio, F. J. (2009) Characterization of an alcohol dehydrogenase from the Cyanobacterium Synechocystis sp. strain PCC 6803 that responds to environmental stress conditions via the Hik34-Rre1 two-component system J. Bacteriol. 191, 4383-91 10.1128/JB.00183-09
33. Trautmann, D., Beyer, P., and Al-Babili, S. (2013) The ORF slr0091 of Synechocystis sp. PCC6803 encodes a high-light induced aldehyde dehydrogenase converting apocarotenals and alkanals FEBS J. 280, 3685-3696 10.1111/febs.12361
34. Anfelt, J., Hallström, B., Nielsen, J., Uhlén, M., and Hudson, E. P. (2013) Using transcriptomics to improve butanol tolerance of Synechocystis sp. strain PCC 6803 Appl. Environ. Microbiol. 79, 7419-27 10.1128/AEM.02694-13
35. Yang, Y., Yin, C., Li, W., and Xu, D. (2008) α-Tocopherol is essential for acquired chill-light tolerance in the cyanobacterium Synechocystis sp. strain PCC 6803 J. Bacteriol. 190, 1554-1560 10.1128/JB.01577-07
36. Mitschke, J., Georg, J., Scholz, I., Sharma, C., Dienst, D., Bantscheff, J., Voss, B., Steglich, C., Wilde, A., Vogel, J., and Hess, W. (2011) An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803 Proc. Natl. Acad. Sci. U. S. A. 108, 2124-2129 10.1073/pnas.1015154108
37. Tyo, K. E., Zhou, H., and Stephanopoulos, G. N. (2006) High-Throughput Screen for Poly-3-Hydroxybutyrate in Escherichia coli and Synechocystis strain PCC6803 Appl. Environ. Microbiol. 72, 3412-3417 10.1128/AEM.72.5.3412-3417.2006
38. Schlebusch, M. and Forchhammer, K. (2010) Requirement of the nitrogen starvation-induced protein Sll0783 for polyhydroxybutyrate accumulation in Synechocystis sp. strain PCC 6803 Appl. Environ. Microbiol. 76, 6101-7 10.1128/AEM.00484-10