David Dryden

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Bacterial DNA restriction and modification
systems structure, function and evolution.

• David Dryden
• School of Chemistry
• University of Edinburgh

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Bacterial DNA restriction and modification
systems structure, function and evolution.
Current group Gareth Roberts, John White,
Laurie Cooper, Ed Bower, Matt Tilling
Collaborators University of Cambridge
Robert Henderson, Mike Edwardson University of
Edinburgh Noreen Murray, Garry Blakely,
Malcolm Walkinshaw, Wilson Poon, Anita
Jones St. George's, University of London
Patrick Houston, Jodi Lindsay University of
Leeds Chris Kennaway, John
Trinick University of Portsmouth James Taylor,
Geoff Kneale University of St. Andrews Jim
Naismith
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Bacterial DNA restriction and modification
systems structure, function and evolution.
1. Restriction and modification (RM) systems and
their inhibition by antirestriction
systems. 2. Type I RM enzymes structure,
function and evolution. 3. Some speculation on
the antiquity of RM systems and their influence
on evolution.
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RM systems control Horizontal Gene Transfer.
Tock and Dryden, Curr. Op. Microbiol. (2005) 8,
466.
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The major classes of RM systems.
REBASE Genomes (4910 Bacteria, 191 Archaea)
There are 11 subtypes of Type II
systems! Also Type III and Type IV systems.
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The major classes of RM systems are Type I and
Type II systems.
The tools of molecular biology are the simplest
Type II restriction enzymes. Nature has evolved
systems of far greater complexity such as the
Type I systems. Type I RM enzymes comprise 5
subunits 1x HsdS binds DNA target 2x HsdM binds
SAM, methylates DNA 2xHsdR hydrolyses ATP,
translocates and cuts DNA
Roberts et al. Nucleic Acids Res. (2003) 31,
1805 Dryden Nature Struct. Mol. Biol. (2005) 11,
804.
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Antirestriction systems such as antirestriction
proteins control RM systems. They co-evolve to
assist Horizontal Gene Transfer.
Antirestriction methods 1. Avoid having target
sites 2. Modified DNA bases 3. Co-injection of
antirestriction proteins 4. Consumption of
cofactors for R/M systems 5. Enhance host
modification activity 6. Proteolysis of RM
enzymes 7. Encode specialised antirestriction
proteins e.g. ArdA and ArdB on conjugative
transposons and plasmids and Ocr on phage T7.
Plus many others as yet poorly characterised.
Ocr from phage T7
Bickle and Kruger, Microbiol. Rev. (1993) 57,
434. Tock and Dryden, Curr. Op. Microbiol.
(2005) 8, 466. Dryden, Trends Biotech. (2006)
24, 378.
Walkinshaw et al. Mol. Cell (2002) 9, 187.
McMahon et al., (2009) Nucl. Acids Res. 37,
4887. Serfiotis-Mitsa et al., (2009) Nucl. Acids
Res. 38,1723.
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Antirestriction systems such as antirestriction
proteins control RM systems.
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Antirestriction systems such as antirestriction
proteins control RM systems.
ArdB from a B. pertussis plasmid
Ocr from phage T7
ArdA from transposon Tn916
Walkinshaw et al. Mol. Cell (2002) 9, 187.
McMahon et al., (2009) Nucl. Acids Res. 37, 4887.
Serfiotis-Mitsa et al., (2010) Nucl. Acids Res.
38, 1723.
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Bacterial DNA restriction and modification
systems structure, function and evolution.
1. Restriction and modification (RM) systems and
their inhibition by antirestriction systems. 2.
Type I RM enzymes structure, function and
evolution. 3. Some speculation on the antiquity
of RM systems and their influence on evolution.
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The components of Type I DNA RM enzymes.
Highly conserved in sequence and structure except
for target recognition domains in the S subunits.
Type I RM enzyme comprises 5 subunits R2M2S1
Molecular mass 440,000
Kennaway et al. Genes and Development (2012) 26,
92-104.
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Type I RM systems in S. aureus allow changes of
specificity.
HsdS
CC group / enzyme Trd1 spacer Trd2
CC1-1 CCAY (N)5 TTAA
CC1-2 CCAY (N)6 TGT
CC5-1 ATC (N)5 CCT
CC5-2 CCAY (N)6 GTA
CC133-771 CAG (N)5 RTGA
CC398-1 ACC (N)5 RTGA
26 other CC 12 others 14 others
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Kennaway et al. Genes and Development (2012) 26,
92-104.
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Type I RM systems in S. aureus control horizontal
gene transfer.
Roberts et al. Nucl. Acids Res. doi
10.1093/nar/gkt535
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Bacterial DNA restriction and modification
systems structure, function and evolution.
1. Restriction and modification (RM) systems and
their inhibition by antirestriction systems. 2.
Type I RM enzymes structure, function and
evolution. 3. Some speculation on the antiquity
of RM systems and their influence on evolution.
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What was the first RM system?
What did the first RM system look like? When
did it appear? What pressure caused it to
diversify? (Antirestriction perhaps?)
Williams. J. Inorg. Biochem. (2006), 100, 1908
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Why was the first RM system not a Type II RM
system? They are too specialised.
Type II restriction enzymes highly variable in
sequence and structure but the methylases are
conserved.
Pingoud and Jeltsch. Nucl Acids Res (2001) 29,
3705 Cheng and Roberts. Nucl Acids Res (2001) 29,
3784
Subtypes of Type II restriction enzymes.
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What was the first RM system? Perhaps it was a
proto-Type I RM enzyme?
The first RM system could be built from DNA
repair enzymes, small-molecule methylases and
transcription factors. These would be present
before the LUCA. Most antirestriction targets
Type I RM systems. This would force
diversification in RM structure to avoid
antirestriction DNA mimics and create new RM
Types.
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What would happen to Horizontal Gene Transfer
with "perfect" restriction and modification
systems or "perfect" antirestriction?
Why did RM and anti-RM appear?