Antirestriction systems

Restriction endonucleases will degrade invading double-stranded phage or plasmid DNA that is not appropriately modified. However, under certain stress conditions (for example, induction of the SOS response or heat shock) restriction endonucleases can be temporarily inactivated [Kelleher and Raleigh 1994; Barcus and Murray 1995]. Furthermore, many phage and plasmids have mechanisms to avoid degradation of their DNA. Such mechanisms are called "antirestriction systems". Some examples of antirestriction systems are described below.

• "Loss" of restriction sites. Some phage have many fewer recognition sites for certain restriction endonucleases than you would predict by random chance. For example, the phages T3 and T7 lack the 5-bp EcoRII recognition site CC(A or T)GG. This is thought to arise by selection for phage with mutations that prevent cleavage by restriction endonucleases commonly encountered in their hosts [Korona et al. 1993; Kruger et al. 1995].

• Modified bases. Some phage have modified bases that prevent recognition by restriction endonucleases. For example, phages T2 and T4 have hydroxylmethylcytosine instead of cytosine in their DNA [Carlson et al. 1994].

• Self-methylation. Some phage encode a methylase that can modify their DNA so that it is not cleaved by certain restriction endonucleases. For example, the E. coli phages T2, T4, and the Myxococcus phage Mx8 encode dAdenine methylases (dam) [Carlson et al. 1994; Magrini et al. 1997]. Certain plasmids also encode methylases that may provide protection against restriction endonucleases [Ibanez et al. 1997].

• Activation of a host methylase. Some phage encode a protein that stimulates the host's methylase to modify the phage DNA. For example, the Lambda Ral ("restriction alleviation") protein enhances methylation by the HsdM subunit of the EcoK and EcoB restriction systems [Court and Oppenheim 1983]. Ral seems to act by stimulating the expression of the host hsdS and hsdM genes [Loenen and Murray 1986].

• Degradation of host S-adensylmethionine. Some host restriction systems only recognize modified DNA (e.g. the McrA and McrB systems in E. coli). Phage T3 encodes a S-adensylmethionine hydrolase activity that degrades the substrate required for methylation by host enzymes, thus avoiding modification of the phage DNA and subsequent cleavage by modification-dependent host endonucleases [Kruger et al. 1985].

• Inhibition of host restriction endonucleases. Many conjugal plasmids produce antirestriction proteins (called Ard) that specifically inhibit Type I restriction endonucleases. The Ard proteins have a motif that is very similar to a motif found in the HsdS subunit, thus it is possible that the Ard proteins prevent proper assembly of the restriction endonuclease complex by binding to the other Hsd subunits [Belogurov and Delver 1995]. Phage T3 produces a protein called Ocr which inhibits host methylases, resulting in resistance to modification-dependent restriction systems [Kruger et al. 1985].

• DNA repair systems. Activity of certain phage genes may allow repair of the double-stranded breaks produced by restriction endonucleases. For example, the lambda Gam and Red proteins may repair the cleaved DNA by recombination with another copy of the phage DNA [Salaj-Smic et al. 1997].

REFERENCES

For a nice recent review see:
Wilkins B. 2002.Plasmid promiscuity: meeting the challenge of DNA immigration control. Environ Microbiol. 4: 495-500.

• Belogurov, A., and E. Delver. 1995. A motif conserved among the type I restriction-modification enzymes and antirestriction proteins: a possible basis for mechanism of action of plasmid-encoded antirestriction functions. Nucleic Acids Res. 23: 785-787.
  
• Barcus, V., and N. Murray. 1995. Barriers to recombination: restriction. In S. Baumberg, J. Young, E. Wellington, and J. Saunders (eds.), Population Genetics of Bacteria, pp. 31-58. University Press, Cambridge.
  
• Carlson, K., E. Raleigh, and S. Hattman. 1994. Restriction and modification. In J. Karam (ed.), Molecular Biology of Bacteriophage T4, pp. 369-381. American Society for Microbiology, Washington, D.C.
  
• Court, D., and A. Oppenheim. 1983. Phage Lambda's accessory genes. In R. Hendrix, J. Roberts, F. Stahl, and R. Weisberg (eds.), Lambda II, pp. 251-277. Cold Spring Harbor Laboratory, NY.
  
• Ibanez, M., I. Alvarez, J. Rodriguez-Pena, and R. Rotger. 1997. A ColE1-type plasmid from Salmonella enteritidis encodes a DNA cytosine methyltransferase. Gene 196: 145-158.
  
• Kelleher, J., and E. Raleigh . 1994. Response to UV damage by four Escherichia coli K-12 restriction systems. J. Bacteriol. 176: 5888-5896.
  
• Korona, R., B. Korona, and B. Levine. 1993. Sensitivity of naturally occuring coliphages to type I and type II restriction and modification. J. Gen. Microbiol. 139: 1283-1290.
  
• Kruger, D., C. Schroeder, M. Reuter, I. Bogdarina, Y. Buryanov, T. Bickle. 1985. DNA methylation of bacterial viruses T3 and T7 by different DNA methylases in Escherichia coli K12 cells. Eur. J. Biochem. 150: 323-330.
  
• Kruger, D., D. Kupper, A. Meisel, M. Reuter, and C. Schroeder. 1995. The significance of distance and orientation of restriction endonuclease recognition sites in viral DNA genomes. FEMS Microbiol. Rev. 17: 177-184.
  
• Loenen, W., and N. Murray. 1986. Modification enhancement by the restriction alleviation protein (Ral) of bacteriophage lambda. J. Mol. Biol. 190: 11-22.
  
• Magrini, V., D. Salmi, D. Thomas, S. Herbert, P. Hartzell, and P. Youderian. 1997. Temperate Myxococcus xanthus phage Mx8 encodes a DNA adenine methylase, Mox. J. Bacteriol. 179: 4254-4263.
  
• Salaj-Smic, E., N. Marsic, Z. Trgovcevic, and R. Lloyd. 1997. Modulation of EcoKI restriction in vivo: role of the lambda Gam protein and plasmid metabolism. J. Bacteriol. 179: 1852-1856.