Two different restriction-modification systems for degrading exogenous DNA in Paenibacillus polymyxa

Accompanied by benefits from horizontally transferred genes, bacteria have to face the risk of the invasion of dangerous genes. Bacteria often use the restriction-modification (R-M) system, which is consisted of methyl transferase (MEase) and restrictase (REase), to protect self-DNA and defend against foreign DNA. Paenibacillus polymyxa, widely used as growth promoting rhizobacteria in agriculture, can also produce compounds of medical and industrial interests. It is unclear whether R-M systems exist in P. polymyxa. In this study, we used a shuttle plasmid with epigenetic modification from different bacteria to explore R-M systems in P. polymyxa. We found that DNA which is methylated by DNA adenine methyltransferase (Dam) in E. coli was strongly restricted, indicating the presence of a Dam-methylation-dependent R-M system in P. polymyxa. Whereas, DNA from a dam-E. coli strain was also moderately restricted, indicating the presence of a Dam-methylation-independent R-M system. Degradation of plasmid DNA with Dam methylation by cell-free protein extract of P. polymyxa provides additional evidence for the presence of Dam-methylation-dependent R-M system. Taken together, our work showed that there are two different types of R-M system in P. polymyxa, providing a foundation for the study of innate immunity in P. polymyxa and for the development of genetic engineering tools in P. polymyxa.