Prokaryotes protect themselves from viruses and mobile genetic elements at several levels. They can produce exopolysaccharide capsules around the cell or slime that covers viral receptors and prevents viral binding. Secreted extracellular enzymes can destroy pathogenic nuclear acids around the cell. After a pathogen enters the cell, it can be destroyed by sugar-nonspecific nucleases that cleave both DNA and RNA. A common defense mechanism is restriction-modification (R/M). R/M systems are based on methylation of the host DNA at specific sequences, whereas viral DNA not protected by methylation is quickly degraded by restriction endonucleases. R/M systems differ in the type of enzymes and recognition principles. Most archaea and half of the bacteria have the prokaryotic adaptive immune system CRISPR-Cas. This system consists of CRISPR (clustered regularly interspersed short palindromic repeats) and CRISPR-associated (Cas) proteins. Other defenses include Argonaute-based systems that utilize both DNA and RNA guides to destroy foreign nucleic acids and abortive infection (Abi), which is a measure of last resort, such that death of the infected cells prevents spread of infection.
Keywords: Abortive infection, Argonaute, Bacteriophage exclusion, CRISPRCas, Extracellular nucleases, Phase variation, Restriction-modification system, Sugar-nonspecific nucleases, Superinfection exclusion.