Restriction-modification system evasion by virus (kw:KW-1258)

The restriction-modification (RM) system is a defense mechanism present in over 90% of sequenced bacterial and archeal genomes. Its consists of a modification enzyme that methylates a specific DNA sequence in a genome and a restriction endonuclease that cleaves DNA lacking this methylation .<div id="PMID: 11782494" class="hidden">2001 Fred Griffith review lecture. Immigration control of DNA in bacteria: self versus non-self
Noreen E Murray
Microbiology (Reading, Engl.) January 2002; 148: 3?20


Bacterial viruses have evolved different strategies to evade the restriction-modification system . Some viruses encode their own methyltransferase in order to protect their genome from host restriction enzymes . Instead, bacteriophage T7 encodes the OCR protein that blocks the active site of several restriction enzymes by mimicking the phosphate backbone of B-form DNA. Other bacterial viruses use unusual bases on their genome to avoid restriction. Bacteriophages SPO1, SP82, and 2C replace thymidine with 5-hydroxymethyluracil while phages PBS1 and PBS2 thymine is completely changed to uracil.

Family Genus Virus Strategy of RM evasion Viral protein Ref.
Siphoviridae Tunalikevirus Bacteriophage T1 Viral methyltransferase Dmt methyltransferase
Podoviridae T7likevirus Bacteriophage T3 Viral SAMase S-adenosyl-L-methionine hydrolase
Myoviridae T4likevirus Bacteriophage T4 Viral methyltransferase Dam methyltransferase
Myoviridae T4likevirus Bacteriophage T2 Viral methyltransferase Dam methyltransferase
Podoviridae T7likevirus Bacteriophage T7 Inhibition of type-I RM enzymes OCR protein
Myoviridae Punalikevirus Bacteriophage P1 Internal capsid protein DarA, DarB
Podoviridae P22likevirus Bacteriophage P22 Modification of host methylase activity Ral
Siphoviridae Lambdalikevirus Bacteriophage λ reverse Modification of host methylase activity Lar
Siphoviridae Lambdalikevirus Bacteriophage λ Modification of host methylase activity Ral
Myoviridae Mulikevirus Bacteriophage Mu Adenine acetyltransferase Mom

Matching UniProtKB/Swiss-Prot entries

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40 entries grouped by strain

5 entries

Enterobacteria phage T4 (Bacteriophage T4) reference strain

DMA_BPT4 DNA adenine methylase (EC (DNA-(N(6)-adenine)-methyltransferase) ...
GSTA_BPT4 DNA alpha-glucosyltransferase (AGT) (Alpha-GT) (EC
GSTB_BPT4 DNA beta-glucosyltransferase (BGT) (Beta-GT) (EC
ARN_BPT4 Anti-restriction endonuclease (Anti-rgl nuclease)
STP_BPT4 T4 Suppressor of prr (Stp)

4 entries

Pseudomonas phage PaMx11 reference strain

GLYDT_BPPAM Glycinyltransferase (Amino acid:DNA transferase) (AADT) (gp46)
AT_BPPAM 5-NmdU N-acetyltransferase
FADL_BPPAM Flavin-dependent lyase (gp47)
HMUDK_BPPAM 5-hmdU DNA kinase (5-hydroxymethyluracil DNA kinase) (P-loop kinase) (gp49)

4 entries

Salmonella phage ViI reference strain

SERDT_BPSAV Serinyltransferase (Amino acid:DNA transferase) (AADT) (gp247)
HMUD1_BPSAV 5-hmdU DNA kinase 1 (5-hydroxymethyluracil DNA kinase) (P-loop kinase) (gp67)
PLP_BPSAV O-seryl-dTMP PLP-dependent decarboxylase
HMUD2_BPSAV 5-hmdU DNA kinase 2 (5-hydroxymethyluracil DNA kinase) (P-loop kinase) (gp243)

3 entries

Delftia phage PhiW-14 (Deftia acidovorans bacteriophage phiW-14) reference strain

HMUDK_BPW14 5-hmdU DNA kinase (5-hydroxymethyluracil DNA kinase) (P-loop kinase) (gp37)
PUTDT_BPW14 Putrescinyltransferase (Amino acid:DNA transferase) (AADT)
DUHM_BPW14 Deoxyuridylate hydroxymethyltransferase (Deoxyuridylate hydroxymethylase) (EC 2.1.2.-) (dUMP ...

3 entries

Escherichia phage P1 (Bacteriophage P1) reference strain

DARB_BPP1 Defense against restriction protein B (EC 3.6.4.-) (DarB)
DAM_BPP1 DNA N-6-adenine-methyltransferase (DAM) (EC (EcoP1I DNA MTase) (M.EcoP1I) (Type II ...
DARA_BPP1 Defense against restriction protein A (DarA)

1 entry

Bacillus phage SP01 (Bacteriophage SP01) reference strain

DUHM_BPSP1 Deoxyuridylate hydroxymethyltransferase (Deoxyuridylate hydroxymethylase) (EC 2.1.2.-) (Gp29) (dUMP ...

1 entry

Bacillus phage SP10 (Bacillus phage SP-10) reference strain

HMUDK_BPS10 5-hmdU DNA kinase (5-hydroxymethyluracil DNA kinase) (P-loop kinase) (gp186)

1 entry

Bacillus phage SPbeta (Bacillus phage SPBc2) (Bacteriophage SP-beta) reference strain

MTBB_BPSPB Orphan methyltransferase M.SPBetaI (M.SPBetaI) (EC (Cytosine-specific methyltransferase ...

1 entry

Escherichia phage Mu (Bacteriophage Mu) reference strain

MOM_BPMU Methylcarbamoylase mom (Adenine modification enzyme mom) (Gene product 55) (gp55) (Gene product mom) ...

1 entry

Escherichia phage T1 (Bacteriophage T1) reference strain

DAM_BPT1 DNA N-6-adenine-methyltransferase (DAM) (EC (Orphan methyltransferase M.EcoT1Dam) ...

1 entry

Escherichia phage T7 (Bacteriophage T7) reference strain

OCR_BPT7 Protein Ocr (Gene product 0.3) (Gp0.3) (Overcome classical restriction) (Ocr)

1 entry

Escherichia phage lambda (Bacteriophage lambda) reference strain

RAL_LAMBD Restriction inhibitor protein ral (Antirestriction protein)

1 entry

Haemophilus phage HP1 (strain HP1c1) (Bacteriophage HP1) reference strain

DAM_BPHC1 DNA N-6-adenine-methyltransferase (DAM) (EC (ORF13) (Orphan methyltransferase M.HinHP1Dam) ...

1 entry

Salmonella phage P22 (Bacteriophage P22) reference strain

RAL_BPP22 Restriction inhibitor protein ral (Antirestriction protein)

6 entries

Pseudomonas phage M6

DUHM_BPPM6 Deoxyuridylate hydroxymethyltransferase (Deoxyuridylate hydroxymethylase) (EC 2.1.2.-) (dUMP ...
DPOLA_BPPM6 DNA-directed DNA polymerase (EC
GLYDT_BPPM6 Glycinyltransferase (Amino acid:DNA transferase) (AADT) (gp51)
RSAMI_BPPM6 Radical SAM Nalpha-GlyT isomerase (gp53) (rSAM glycinyl-thymine isomerase)
HMUDK_BPPM6 5-hmdU DNA kinase (5-hydroxymethyluracil DNA kinase) (P-loop kinase) (gp54)
PLP_BPPM6 Glycyl-dTMP PLP-dependent decarboxylase (gp52)

1 entry

Bacillus phage SPR (Bacteriophage SPR)

MTBS_BPSPR Orphan methyltransferase M.SPRI (M.SPRI) (EC (Cytosine-specific methyltransferase SPRI) ...

1 entry

Bacillus phage phi3T (Bacteriophage phi-3T)

MTBP_BPPHT Orphan methyltransferase M.Phi3TI (M.Phi3TI) (EC (Cytosine-specific methyltransferase ...

1 entry

Bacillus phage rho11s (Bacteriophage rho-11s)

MTBR_BPRH1 Orphan methyltransferase M.Rho11sI (M.Rho11sI) (EC (Bsu P11s) (Cytosine-specific ...

1 entry

Enterobacteria phage T2 (Bacteriophage T2)

DMA_BPT2 DNA adenine methylase (EC (DNA-(N(6)-adenine)-methyltransferase) ...

1 entry

Enterobacteria phage phi21 (Bacteriophage phi-21)

RAL_BPPH3 Restriction inhibitor protein ral (Antirestriction protein)

1 entry

Escherichia phage D108 (Bacteriophage D108)

MOM_BPD10 Methylcarbamoylase mom (Adenine modification enzyme mom) (Gene product mom) (gpMom) (Modification of ...