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ACS Synth Biol. 2018 Apr 20;7(4):1085-1094. doi: 10.1021/acssynbio.7b00462. Epub 2018 Mar 21.

High-Level dCas9 Expression Induces Abnormal Cell Morphology in Escherichia coli.

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Department of Biological Sciences and KI for the BioCentury , Korea Advanced Institute of Science and Technology , Daejeon 305-701 , Republic of Korea.
Intelligent Synthetic Biology Center , Daejeon 305-701 , Republic of Korea.
Department of Bioengineering , University of California San Diego , La Jolla , California 92122 , United States.
Department of Pediatrics , University of California San Diego , La Jolla , California 92122 , United States.


Along with functional advances in the use of CRISPR/Cas9 for genome editing, endonuclease-deficient Cas9 (dCas9) has provided a versatile molecular tool for exploring gene functions. In principle, differences in cell phenotypes that result from the RNA-guided modulation of transcription levels by dCas9 are critical for inferring with gene function; however, the effect of intracellular dCas9 expression on bacterial morphology has not been systematically elucidated. Here, we observed unexpected morphological changes in Escherichia coli mediated by dCas9, which were then characterized using RNA sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq). Growth rates were severely decreased, to approximately 50% of those of wild type cells, depending on the expression levels of dCas9. Cell shape was changed to abnormal filamentous morphology, indicating that dCas9 affects bacterial cell division. RNA-Seq revealed that 574 genes were differentially transcribed in the presence of high expression levels of dCas9. Genes associated with cell division were upregulated, which was consistent with the observed atypical morphologies. In contrast, 221 genes were downregulated, and these mostly encoded proteins located in the cell membrane. Further, ChIP-Seq results showed that dCas9 directly binds upstream of 37 genes without single-guide RNA, including fimA, which encodes bacterial fimbriae. These results support the fact that dCas9 has critical effects on cell division as well as inner and outer membrane structure. Thus, to precisely understand gene functions using dCas9-driven transcriptional modulation, the regulation of intracellular levels of dCas9 is pivotal to avoid unexpected morphological changes in E. coli.


CRISPR/CAS; cell division; cell morphology; dCas9; gene editing


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