E. coli restriction-modification system: Difference between revisions
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Brief notes of relevance to me taken from [[Escherichia coli & Salmonella]] | '''General Information''' | ||
Brief notes of relevance to me taken from [[Escherichia coli & Salmonella]] and [http://ecocyc.org ecocyc] | |||
*Restriction systems are only found in unicellular organisms. | *Restriction systems are only found in unicellular organisms. | ||
**Either the cell modifies certain sequences so they are not restricted (classic R-M systems) | **Either the cell modifies certain sequences so they are not restricted (classic R-M systems) | ||
**or certain foreign modifications are restricted. | **or certain foreign modifications are restricted. | ||
*'''Mcr Systems''' | *'''''E. Coli'' K12 (MG1655) restriction systems''' | ||
**According to information from [http://ecocyc.org Ecocyc] and [[Escherichia coli & Salmonella]], the following restriction enzymes are found in ''E. coli'' K12. | |||
**Contains the type I restriction enzyme EcoK encoded by hsdR - cleaves -AAC(N<sub>6</sub>)GTCG- if the second A is unmethylated. | |||
**Contains the Mcr systems described below. These restriction systems do not appear to have a recognition sequence, they just cut at the methylated residues. | |||
**Contains the Mrr system which cleaves m6A or m5c residues. The sequence specificity is unknown. | |||
*'''Mcr Systems (found in ''E. coli'' strains)''' | |||
**''McrBC'' - cleaves hm5C, m5C and m4C (hydroxymethylated or methylated cytosine at positions 4 or 5). The modified bases must be paired about 40-80bp apart. (genes ''mcrB'' and ''mcrC'') | **''McrBC'' - cleaves hm5C, m5C and m4C (hydroxymethylated or methylated cytosine at positions 4 or 5). The modified bases must be paired about 40-80bp apart. (genes ''mcrB'' and ''mcrC'') | ||
**''McrA'' - cleaves DNA methylated by HpaII and SssI methylases. (encoded by the prophagelike e14 element) | **''McrA'' - cleaves DNA methylated by HpaII and SssI methylases. (encoded by the prophagelike e14 element) | ||
==Classic R-M systems== | |||
''A classic R-M system includes an endonuclease that cleaves a specific DNA sequence and a DNA methyltransferase that methylates either adenosyl or cytosyl residues within the same DNA sequence.'' | ''A classic R-M system includes an endonuclease that cleaves a specific DNA sequence and a DNA methyltransferase that methylates either adenosyl or cytosyl residues within the same DNA sequence.'' | ||
*'''Type I R-M systems''' | *'''Type I R-M systems''' |
Revision as of 13:04, 31 July 2005
General Information Brief notes of relevance to me taken from Escherichia coli & Salmonella and ecocyc
- Restriction systems are only found in unicellular organisms.
- Either the cell modifies certain sequences so they are not restricted (classic R-M systems)
- or certain foreign modifications are restricted.
- E. Coli K12 (MG1655) restriction systems
- According to information from Ecocyc and Escherichia coli & Salmonella, the following restriction enzymes are found in E. coli K12.
- Contains the type I restriction enzyme EcoK encoded by hsdR - cleaves -AAC(N6)GTCG- if the second A is unmethylated.
- Contains the Mcr systems described below. These restriction systems do not appear to have a recognition sequence, they just cut at the methylated residues.
- Contains the Mrr system which cleaves m6A or m5c residues. The sequence specificity is unknown.
- Mcr Systems (found in E. coli strains)
- McrBC - cleaves hm5C, m5C and m4C (hydroxymethylated or methylated cytosine at positions 4 or 5). The modified bases must be paired about 40-80bp apart. (genes mcrB and mcrC)
- McrA - cleaves DNA methylated by HpaII and SssI methylases. (encoded by the prophagelike e14 element)
Classic R-M systems
A classic R-M system includes an endonuclease that cleaves a specific DNA sequence and a DNA methyltransferase that methylates either adenosyl or cytosyl residues within the same DNA sequence.
- Type I R-M systems
- Relatively rare.
- One, three-subunit protein acts as both endonuclease and methylase.
- Requires AdoMet as a cofactor.
- Endonuclease activity also requires Mg2+ and ATP.
- E. coli has a type 1 restriction system encoded by hsdR, hsdM, and hsdS.
- Type II R-M systems
- Relatively abundant - these are the restriction enzymes found in the NEB catalog etc.
- Separate nuclease and methylation enzymes.
- Requires AdoMet as a cofactor.
- Endonuclease activity also requires Mg2+
- Little homology between restriction and methylation enzymes despite the shared DNA recognition sequence.
- Most recognition sequences are close to symmetric.
- Endonucleases normally act as homodimers, acting on sense and anti-sense strands.
- A subgroup of Type II restriction enzymes (Type IIS) cleave a fixed distance away from the recognition sequence.
- Type III R-M systems
- Relatively rare.
- Hetero-oligomeric protein catalyzes both the restriction and modification reactions.
- Requires AdoMet as a cofactor for modification.
- Endonuclease activity also requires Mg2+ and ATP.
- Encoded by mod and res genes in E. coli.
- Only one strand is methylated unlike the other systems.
- The restriction enzyme requires two recognition sites in inverse orientation.
- Regulation
- There is no evidence of transcriptional regulation of Type I R-M systems in E. coli
- However, there must be some regulation as the modification subunit is always expressed before the restriction subunit.
- There is little clear information about the regulation of Type II R-M systems, in part because many of them come from poorly understood bacteria.
- Type II R-M regulation is also not very well understood. However, the modification enzyme is again expressed prior to the restriction enzyme.