1. Mechanism of horizontal gene transfer

Horizontal gene transfer drives evolution of bacteria. As one of the main HGT forms, natural transformation plays an important role in spreading antibiotic resistance genes (ARGs). Many bacteria are able to acquire ARGs through a conserved machinenary which allows the entry of single-stranded DNA. Our study reveals that Escherichia coli is naturally transformable and regulated by the general stress response regulator RpoS. However, the conserved DNA uptake gene homologs do not mediate natural plasmid transformation. Instead, double-stranded DNA was taken up into the cell in the form of double-stranded DNA. Besides, we showed that the antibiotic resistance NDM-1 superplasmid was able to spread in soil bacteria, emphasizing the significance of plasmid transfer in the formation of bacterial resistance in environment.

2. Regulation of CRISPR defence and application of CRISPR-Cas system

The CRISPR-based defense system protects prokaryotes against invading plasmids and viruses by memorizing their nucleotide-sequence traits and destructing the nucleic acids. Although working mechanisms of CRISPR-Cas systems have been well defined, our understanding of its regulation remains incomplete. Our work demonstrate that the histone like nucleoid protein StpA activates the type I-E CRISPR-Cas system against natural transformation of E. coli. We also identified a new LysR type regulator LrhA as an activator of the type I-E CRISPR-Cas system in E. coli. Additionally, we re-established the type I-E CRISPR-Cas system in a probiotic E. coli Nissle 1917 to block transfer of ARGs, and in B. subtilis to modulate expression of a key metabolic gene for balancing the metabolic flux toward TCA cycle and biosynthesis of D-Pantothetic acid.