Next Generation Prokaryotic Engineering: The CRISPR-Cas Toolkit

Ioannis Mougiakos, Elleke F. Bosma, Willem M. de Vos, Richard van Kranenburg, John van der Oost*

*Corresponding author for this work

Research output: Contribution to journalReviewpeer-review


The increasing demand for environmentally friendly production processes of green chemicals and fuels has stimulated research in microbial metabolic engineering. CRISPR-Cas-based tools for genome editing and expression control have enabled fast, easy, and accurate strain development for established production platform organisms, such as Escherichia coli and Saccharomyces cerevisiae. However, the growing interest in alternative production hosts, for which genome editing options are generally limited, requires further developing such engineering tools. In this review, we discuss established and emerging CRISPR-Cas-based tools for genome editing and transcription control of model and non-model prokaryotes, and we analyse the possibilities for further improvement and expansion of these tools for next generation prokaryotic engineering. SpyCas9 has recently been established as an efficient counterselection system in combination with homologous recombination-based strategies for bacterial genome editing.Besides the traditionally used SpyCas9, other CRISPR-Cas systems (both heterologous and native) are currently being evaluated in bacteria for their editing potential.Catalytically inactive variants of CRISPR-Cas systems are used for transcriptional control in bacteria with great potential for fundamental research and applications.

Original languageEnglish
JournalTrends in Biotechnology
Issue number7
Pages (from-to)575-587
Number of pages13
Publication statusPublished - 2016
Externally publishedYes


  • Archaea
  • Bacteria
  • Cas9
  • CRISPR-Cas
  • Genome editing
  • Recombineering

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