Efficiency of the synthetic self‐splicing RiboJ ribozyme is robust to cis‐ and trans‐changes in genetic background

The expanding knowledge of the variety of synthetic genetic elements has enabled the construction of new and more efficient genetic circuits and yielded novel insights into molecular mechanisms. However, context dependence, in which interactions between cis‐ or trans‐genetic elements affect the behavior of these elements, can reduce their general applicability or predictability. Genetic insulators, which mitigate unintended context‐dependent cis‐interactions, have been used to address this issue. One of the most commonly used genetic insulators is a self‐splicing ribozyme called RiboJ, which can be used to decouple upstream 5′ UTR in mRNA from downstream sequences (e.g., open reading frames). Despite its general use as an insulator, there has been no systematic study quantifying the efficiency of RiboJ splicing or whether this autocatalytic activity is robust to trans‐ and cis‐genetic context. Here, we determine the robustness of RiboJ splicing in the genetic context of six widely divergent E. coli strains. We also check for possible cis‐effects by assessing two SNP versions close to the catalytic site of RiboJ. We show that mRNA molecules containing RiboJ are rapidly spliced even during rapid exponential growth and high levels of gene expression, with a mean efficiency of 98%. We also show that neither the cis‐ nor trans‐genetic context has a significant impact on RiboJ activity, suggesting this element is robust to both cis‐ and trans‐genetic changes.
Genetic insulators, such as RiboJ self‐splicing ribozyme, have been used to mitigate unintended context‐dependent cis‐interactions when designing genetic circuits. Despite the general use of RiboJ as an insulator, there has been no study quantifying the RiboJ splicing efficiency or whether this autocatalytic activity is robust to trans‐ and cis‐genetic context. Here, we show that mRNA molecules containing RiboJ are spliced with a mean efficiency of 98% and neither the cis‐ nor trans‐genetic context has a significant impact on RiboJ activity.