Bacterial synthetic biology: tools for novel drug discovery

Genetically engineered bacteria as inflammatory bowel disease therapeutics

Inflammatory bowel disease (IBD) is a chronic and recurrent disease caused by immune response disorders that disrupt the intestinal lumen symbiotic ecosystem and dysregulate mucosal immune functions. Current therapies available for IBD primarily focus on symptom management, making early diagnosis and prompt intervention challenging. The development of genetically engineered bacteria using synthetic biology presents a new strategy for addressing these challenges. In this review, we present recent breakthroughs in the field of engineered bacteria for the treatment and detection of IBD and describe how bacteria can be genetically modified to produce therapeutic molecules or execute diagnostic functions. In particular, we discuss the challenges faced in translating live bacterial therapeutics from bacterial design to delivery strategies for further clinical applications.

Transformation-associated recombination (TAR) cloning and its applications for gene function; genome architecture and evolution; biotechnology and biomedicine

Transformation-associated recombination (TAR) cloning represents a unique tool to selectively and efficiently recover a given chromosomal segment up to several hundred kb in length from complex genomes (such as animals and plants) and simple genomes (such as bacteria and viruses). The technique exploits a high level of homologous recombination in the yeast Sacharomyces cerevisiae. In this review, we summarize multiple applications of the pioneering TAR cloning technique, developed previously for complex genomes, for functional, evolutionary, and structural studies, and extended the modified TAR versions to isolate biosynthetic gene clusters (BGCs) from microbes, which are the major source of pharmacological agents and industrial compounds, and to engineer synthetic viruses with novel properties to design a new generation of vaccines. TAR cloning was adapted as a reliable method for the assembly of synthetic microbe genomes for fundamental research. In this review, we also discuss how the TAR cloning in combination with HAC (human artificial chromosome)- and CRISPR-based technologies may contribute to the future.