Restriction-modification system evasion by virus

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

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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

(all links/actions below point to uniprot.org website)

40 entries grouped by protein (browse by keywords)

1 entry

Anti-restriction endonuclease (Anti-rgl nuclease)

ARN_BPT4
Enterobacteria phage T4 (Bacteriophage T4) reference strain

1 entry

5-NmdU N-acetyltransferase

AT_BPPAM
Pseudomonas phage PaMx11

3 entries

DNA N-6-adenine-methyltransferase (DAM) (EC 2.1.1.72) (EcoP1I DNA MTase) (M.EcoP1I) (Type II methyltransferase M.EphP1ORF2P) (M.EphP1ORF2P)

Select_allDeselect_all
DAM_BPHC1
Haemophilus phage HP1 (strain HP1c1) (Bacteriophage HP1) reference strain

DNA N-6-adenine-methyltransferase (DAM) (EC 2.1.1.72) (ORF13) (Orphan methyltransferase M.HinHP1Dam) (M.HinHP1Dam)

DAM_BPP1
Escherichia phage P1 (Bacteriophage P1) reference strain
DAM_BPT1
Escherichia phage T1 (Bacteriophage T1) reference strain

DNA N-6-adenine-methyltransferase (DAM) (EC 2.1.1.72) (Orphan methyltransferase M.EcoT1Dam) (M.EcoT1Dam)

1 entry

Defense against restriction protein A (DarA)

DARA_BPP1
Escherichia phage P1 (Bacteriophage P1) reference strain

1 entry

Defense against restriction protein B (EC 3.6.4.-) (DarB)

DARB_BPP1
Escherichia phage P1 (Bacteriophage P1) reference strain

2 entries

DNA adenine methylase (EC 2.1.1.72) (DNA-(N(6)-adenine)-methyltransferase) (Deoxyadenosyl-methyltransferase) (Orphan methyltransferase M.EcoT2Dam) (M.EcoT2Dam)

Select_allDeselect_all
DMA_BPT4
Enterobacteria phage T4 (Bacteriophage T4) reference strain

DNA adenine methylase (EC 2.1.1.72) (DNA-(N(6)-adenine)-methyltransferase) (Deoxyadenosyl-methyltransferase) (Orphan methyltransferase M.EcoT4Dam) (M.EcoT4Dam)

DMA_BPT2
Enterobacteria phage T2 (Bacteriophage T2)

1 entry

DNA-directed DNA polymerase (EC 2.7.7.7)

DPOLA_BPPM6
Pseudomonas phage M6

3 entries

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

Select_allDeselect_all
DUHM_BPSP1
Bacillus phage SP01 (Bacteriophage SP01) reference strain
DUHM_BPW14
Delftia phage PhiW-14 (Deftia acidovorans bacteriophage phiW-14) reference strain

Deoxyuridylate hydroxymethyltransferase (Deoxyuridylate hydroxymethylase) (EC 2.1.2.-) (dUMP hydroxymethylase) (dUMP-HMase)

DUHM_BPPM6
Pseudomonas phage M6

Deoxyuridylate hydroxymethyltransferase (Deoxyuridylate hydroxymethylase) (EC 2.1.2.-) (dUMP hydroxymethylase) (dUMP-HMase) (gp58)

1 entry

Flavin-dependent lyase (gp47)

FADL_BPPAM
Pseudomonas phage PaMx11

2 entries

Glycinyltransferase (Amino acid:DNA transferase) (AADT) (gp46)

Select_allDeselect_all
GLYDT_BPPAM
Pseudomonas phage PaMx11
GLYDT_BPPM6
Pseudomonas phage M6

Glycinyltransferase (Amino acid:DNA transferase) (AADT) (gp51)

1 entry

DNA alpha-glucosyltransferase (AGT) (Alpha-GT) (EC 2.4.1.26)

GSTA_BPT4
Enterobacteria phage T4 (Bacteriophage T4) reference strain

1 entry

DNA beta-glucosyltransferase (BGT) (Beta-GT) (EC 2.4.1.27)

GSTB_BPT4
Enterobacteria phage T4 (Bacteriophage T4) reference strain

1 entry

5-hmdU DNA kinase 1 (5-hydroxymethyluracil DNA kinase) (P-loop kinase) (gp67)

HMUD1_BPSAV
Salmonella phage ViI reference strain

1 entry

5-hmdU DNA kinase 2 (5-hydroxymethyluracil DNA kinase) (P-loop kinase) (gp243)

HMUD2_BPSAV
Salmonella phage ViI reference strain

4 entries

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

Select_allDeselect_all
HMUDK_BPS10
Bacillus phage SP10 (Bacillus phage SP-10) reference strain
HMUDK_BPW14
Delftia phage PhiW-14 (Deftia acidovorans bacteriophage phiW-14) reference strain

5-hmdU DNA kinase (5-hydroxymethyluracil DNA kinase) (P-loop kinase) (gp37)

HMUDK_BPPAM
Pseudomonas phage PaMx11

5-hmdU DNA kinase (5-hydroxymethyluracil DNA kinase) (P-loop kinase) (gp49)

HMUDK_BPPM6
Pseudomonas phage M6

5-hmdU DNA kinase (5-hydroxymethyluracil DNA kinase) (P-loop kinase) (gp54)

2 entries

Methylcarbamoylase mom (Adenine modification enzyme mom) (Gene product 55) (gp55) (Gene product mom) (gpMom) (Modification of Mu) (Mom)

Select_allDeselect_all
MOM_BPMU
Escherichia phage Mu (Bacteriophage Mu) reference strain
MOM_BPD10
Escherichia phage D108 (Bacteriophage D108)

Methylcarbamoylase mom (Adenine modification enzyme mom) (Gene product mom) (gpMom) (Modification of Mu) (Mom)

1 entry

Orphan methyltransferase M.SPBetaI (M.SPBetaI) (EC 2.1.1.37) (Cytosine-specific methyltransferase SPBetaI) (Modification methylase SPBetaI)

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

1 entry

Orphan methyltransferase M.Phi3TI (M.Phi3TI) (EC 2.1.1.37) (Cytosine-specific methyltransferase Phi3TI) (Modification methylase Phi3TI)

MTBP_BPPHT
Bacillus phage phi3T (Bacteriophage phi-3T)

1 entry

Orphan methyltransferase M.Rho11sI (M.Rho11sI) (EC 2.1.1.37) (Bsu P11s) (Cytosine-specific methyltransferase Rho11sI) (Modification methylase Rho11sI)

MTBR_BPRH1
Bacillus phage rho11s (Bacteriophage rho-11s)

1 entry

Orphan methyltransferase M.SPRI (M.SPRI) (EC 2.1.1.37) (Cytosine-specific methyltransferase SPRI) (Modification methylase SPRI)

MTBS_BPSPR
Bacillus phage SPR (Bacteriophage SPR)

1 entry

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

OCR_BPT7
Escherichia phage T7 (Bacteriophage T7) reference strain

2 entries

Glycyl-dTMP PLP-dependent decarboxylase (gp52)

Select_allDeselect_all
PLP_BPSAV
Salmonella phage ViI reference strain

O-seryl-dTMP PLP-dependent decarboxylase

PLP_BPPM6
Pseudomonas phage M6

1 entry

Putrescinyltransferase (Amino acid:DNA transferase) (AADT)

PUTDT_BPW14
Delftia phage PhiW-14 (Deftia acidovorans bacteriophage phiW-14) reference strain

3 entries

Restriction inhibitor protein ral (Antirestriction protein)

Select_allDeselect_all
RAL_BPP22
Salmonella phage P22 (Bacteriophage P22) reference strain
RAL_LAMBD
Escherichia phage lambda (Bacteriophage lambda) reference strain
RAL_BPPH3
Enterobacteria phage phi21 (Bacteriophage phi-21)

1 entry

Radical SAM Nalpha-GlyT isomerase (gp53) (rSAM glycinyl-thymine isomerase)

RSAMI_BPPM6
Pseudomonas phage M6

1 entry

Serinyltransferase (Amino acid:DNA transferase) (AADT) (gp247)

SERDT_BPSAV
Salmonella phage ViI reference strain

1 entry

T4 Suppressor of prr (Stp)

STP_BPT4
Enterobacteria phage T4 (Bacteriophage T4) reference strain