Exploiting endogenous CRISPR-Cas system for multiplex genome editing in Clostridium tyrobutyricum and engineer the strain for high-level butanol production

Jie Zhang; Wenming Zong; Wei Hong; Zhong-Tian Zhang; Yi Wang

doi:10.1016/j.ymben.2018.03.007

Exploiting endogenous CRISPR-Cas system for multiplex genome editing in Clostridium tyrobutyricum and engineer the strain for high-level butanol production

Metab Eng. 2018 May:47:49-59. doi: 10.1016/j.ymben.2018.03.007. Epub 2018 Mar 9.

Authors

Jie Zhang¹, Wenming Zong², Wei Hong³, Zhong-Tian Zhang¹, Yi Wang⁴

Affiliations

¹ Department of Biosystems Engineering, Auburn University, Auburn, AL 36849, USA.
² Department of Biosystems Engineering, Auburn University, Auburn, AL 36849, USA; School of Engineering, Anhui Agricultural University, Hefei 230036, China.
³ Department of Biosystems Engineering, Auburn University, Auburn, AL 36849, USA; Key Laboratory of Endemic and Ethnic Diseases (Guizhou Medical University), Ministry of Education, Guiyang 550000, China.
⁴ Department of Biosystems Engineering, Auburn University, Auburn, AL 36849, USA; Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL 36849, USA. Electronic address: yiwang3@auburn.edu.

PMID: 29530750
DOI: 10.1016/j.ymben.2018.03.007

Abstract

Although CRISPR-Cas9/Cpf1 have been employed as powerful genome engineering tools, heterologous CRISPR-Cas9/Cpf1 are often difficult to introduce into bacteria and archaea due to their severe toxicity. Since most prokaryotes harbor native CRISPR-Cas systems, genome engineering can be achieved by harnessing these endogenous immune systems. Here, we report the exploitation of Type I-B CRISPR-Cas of Clostridium tyrobutyricum for genome engineering. In silico CRISPR array analysis and plasmid interference assay revealed that TCA or TCG at the 5'-end of the protospacer was the functional protospacer adjacent motif (PAM) for CRISPR targeting. With a lactose inducible promoter for CRISPR array expression, we significantly decreased the toxicity of CRISPR-Cas and enhanced the transformation efficiency, and successfully deleted spo0A with an editing efficiency of 100%. We further evaluated effects of the spacer length on genome editing efficiency. Interestingly, spacers ≤ 20 nt led to unsuccessful transformation consistently, likely due to severe off-target effects; while a spacer of 30-38 nt is most appropriate to ensure successful transformation and high genome editing efficiency. Moreover, multiplex genome editing for the deletion of spo0A and pyrF was achieved in a single transformation, with an editing efficiency of up to 100%. Finally, with the integration of the alcohol dehydrogenase gene (adhE1 or adhE2) to replace cat1 (the key gene responsible for butyrate production and previously could not be deleted), two mutants were created for n-butanol production, with the butanol titer reached historically record high of 26.2 g/L in a batch fermentation. Altogether, our results demonstrated the easy programmability and high efficiency of endogenous CRISPR-Cas. The developed protocol herein has a broader applicability to other prokaryotes containing endogenous CRISPR-Cas systems. C. tyrobutyricum could be employed as an excellent platform to be engineered for biofuel and biochemical production using the CRISPR-Cas based genome engineering toolkit.

Keywords: Butanol; CRISPR-Cas9; CRISPR-Cpf1; Clostridium tyrobutyricum; Endogenous CRISPR-Cas system; Multiplex genome editing.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

1-Butanol / metabolism*
CRISPR-Cas Systems*
Clostridium tyrobutyricum* / genetics
Clostridium tyrobutyricum* / metabolism
Gene Editing / methods*
Metabolic Engineering / methods*

Substances

1-Butanol