Integration-coupled activation of promoterless combinatorial pathway libraries in Clostridium avoids burden during DNA assembly

Abstract

Combinatorial DNA design and assembly is an efficient and pragmatic way to obtain high-performing metabolic pathway designs quickly. However, implementation may require organism-specific technical barriers to be overcome. Firstly, suitable expression control parts such as promoters and ribosome-binding sites (RBSs) which provide a suitable range of expression levels need to be identified or developed. Secondly, these need to be assembled into pathway-encoding combinatorial libraries of sufficient size, quality and diversity. For organisms with transformation frequencies too low to allow direct transformation of library assembly reactions, such as many Clostridium spp., assembly and amplification is typically carried out using Escherichia coli. However, if constructs are deleterious (or burdensome) to E. coli, which is often the case when using Clostridium genetic parts, poor libraries may be obtained. Here we develop a new approach called integration-coupled activation of promoterless sequences (ICAPS) to overcome this barrier and therefore enable combinatorial assembly in Clostridium. Libraries were designed and assembled as promoterless synthetic operons, preventing expression during DNA assembly, and expression was only activated later, when constructs were integrated into the host genome downstream of a promoter. Variation of expression levels was achieved using a range of context-resistant RBS sequences. This approach was used to produce a Clostridium acetobutylicum library with combinatorial expression variants of an introduced hexanol pathway. This proof of concept provides a generally-applicable approach to implement combinatorial metabolic pathway-encoding libraries in Clostridium spp., circumventing the excessive strength of Clostridium expression control parts in E. coli, and is applicable to other organisms.