Recognition sequences of restriction endonucleases and methylases — a review

Keßler, Christoph; Neumaier, Peter S.; Wolf, W. Asher

doi:10.1016/0378-1119(85)90119-2

Cited by 116 publications

(50 citation statements)

References 274 publications

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“…Although about 600 restriction endonucleases with a min- imum of 116 different specificities have been found in a wide variety of procaryotes (13,18), similar enzymes are rare in eucaryotes. A few DNA site-specific endonucleases have been reported in the yeasts Saccharomyces cerevisiae and Pichia membranaefaciens (32,33) and the alga Chlamydomonas reinhardtii (6).…”

Section: Resultsmentioning

confidence: 99%

Restriction endonuclease activity induced by PBCV-1 virus infection of a Chlorella-like green alga.

Xia¹,

Burbank²,

Uher³

et al. 1986

Mol. Cell. Biol.

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An enzyme was isolated from a eucaryotic, ChloreUla-like green alga infected with the virus PBCV-1 which exhibits type II restriction endonuclease activity. The enzyme recognized the sequence GATC and cleaved DNA 5' to the G. Methylation of deoxyadenosine in the GATC sequence inhibited enzyme activity. In vitro the enzyme cleaved host Chlorella nuclear DNA but not viral DNA because host DNA contains GATC and PBCV-1 DNA contains GmATC sequences. PBCV-1 DNA is probably methylated in vivo by the PBCV-1-induced methyltransferase described elsewhere (Y. Xia and J. L. Van Etten, Mol. Cell. Biol. 6:1440 1445). Restriction endonuclease activity was first detected 30 to 60 min after viral infection; the appearance of enzyme activity required de novo protein synthesis, and the enzyme is probably virus encoded. Appearance of enzyme activity coincided with the onset of host DNA degradation after PBCV-1 infection. We propose that the PBCV-1-induced restriction endonuclease participates in host DNA degradation and is part of a virus-induced restriction and modification system in PBCV-1-infected Chlorella cells.We have previously characterized a large polyhedral virus, PBCV-1, which infects and replicates in a unicellular, eucaryotic Chlorella-like green alga, strain NC64A. The virus contains a large double-stranded DNA genome (ca. 300 kilobase pairs as estimated by summing restriction fragments), at least 50 structural proteins, and a lipid component (22,29). The virus can be assayed by plaque formation, and milligram quantities can be produced in culture (27, 28). PBCV-1 infection is synchronous, and progeny virus is first released at 3 to 4 h postinfection; by 6 to 8 h virus release is complete. The virus has a burst size of 200 to 350 PFU per cell (28).Studies on DNA synthesis after PBCV-1 infection established that viral DNA synthesis begins about 45 min after infection; host DNA synthesis ceases immediately after infection, and host nuclear and chloroplast DNAs are degraded beginning about 60 min after infection (26). Base analyses of Chlorella nuclear and PBCV-1 DNAs revealed that the host DNA contains 21% 5-methyldeoxycytidine

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Section: Resultsmentioning

confidence: 99%

Restriction endonuclease activity induced by PBCV-1 virus infection of a Chlorella-like green alga.

Xia¹,

Burbank²,

Uher³

et al. 1986

Mol. Cell. Biol.

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“…There is only one characterized type I 1 restriction enzyme in Lactococcus, ScrFI (Fitzgerald et al, 1982). However isoschizomers, such as BstNI and SmaI which do not cut the lactococcal phage c6A (Powell & Davidson, 1986;Powell et al, 1989), have been found in species of non-lactic streptococci, Staphylococcus and Bacillus (Kessler et al, 1985). These genera are closely related (Stackebrandt & Woese, 1981) so similar specificities could be present in the lactic streptococci.…”

Section: Discussionmentioning

confidence: 99%

Characterization of the prolate-headed lactococcal bacteriophage OvML3: location of the lysin gene and its DNA homology with other prolate-headed phages

Shearman

Hertwig

Teuber

et al. 1991

Journal of General Microbiology

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4vML3 is a virulent prolate-headed bacteriophage that attacks a genetically well-studied strain family including Lactococcus Iactis subsp. Iactis strains 712, C2 and ML3. A restriction map was constructed for &ML3 using a wide variety of restriction endonucleases. The DNA was highly refractory to in uitro restriction; this is a common feature of lytic lactococcal phages. Genome size was estimated as 23 kb, which is similar to the sizes of other phages of the same morphological group. The presence of heat-dissociable DNA fragments was noted in gel electrophoresis of restriction enzyme digests. Cohesive ends were confirmed by pretreating the DNA with T4 ligase, which rendered the composite fragment insensitive to heat. The phage &ML3 genome thus consists of linear and non-permuted double-stranded DNA with complementary cohesive ends. The lysin gene from this phage acts as a specific lysis agent against the lactic streptococci. This gene has been cloned and sequenced previously. Further specific subcloning of EcoRV fragments of &ML3 DNA has located the lysin gene in the central region of the genome, orientated from right to left. This location was confirmed by hybridization of a lysin gene probe to @ML3 DNA. The lysin gene probe showed homology to a number of other prolate-headed phages including Pool. The lysin gene of PO01 was shown to be located in the central region of its genome. However, the isometric phage P107 did not hybridize, in spite of encoding its own lysin gene.

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“…Hpa II does not cut when the internal cytosine is methylated. 49 High-molecular-weight DNA (5 g) was digested for 24 hours with 10 units of either Msp I or Hpa II per microgram of DNA. The DNA fragments were separated by electrophoresis, transferred to nitrocellulose membranes, and hybridized with 32 P-labeled DNA probes.…”

Section: Methylation-specific Pcr and Combined Bisulfite Restriction mentioning

confidence: 99%

Expression of mRNA for DNA methyltransferases and methyl-CpG–binding proteins and DNA methylation status on CpG islands and pericentromeric satellite regions during human hepatocarcinogenesis

2001

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To evaluate the significance of alterations in DNA methylation during human hepatocarcinogenesis, we examined levels of mRNA for DNA methyltransferases and methylCpG-binding proteins and the DNA methylation status in 67 hepatocellular carcinomas (HCCs). The average level of mRNA for DNMT1 and DNMT3a was significantly higher in noncancerous liver tissues showing chronic hepatitis or cirrhosis than in histologically normal liver tissues, and was even higher in HCCs. Significant overexpression of DNMT3b and reduced expression of DNMT2 were observed in HCCs compared with the corresponding noncancerous liver tissues. DNA hypermethylation on CpG islands of the p16 (8% and 66%) and hMLH1 (0% and 0%) genes and methylated in tumor (MINT) 1 (6% and 34%), 2 (24% and 58%), 12 (21% and 33%), 25 (0% and 5%), and 31 (0% and 23%) clones, and DNA hypomethylation on satellites 2 and 3 (18% and 67%), were detected in noncancerous liver tissues and HCCs, respectively. There was no significant correlation between the expression level of any DNA methyltransferase and DNA methylation status. Reduced expression of DNA repair protein, MBD4, was significantly correlated with poorer tumor differentiation and involvement of portal vein. Slightly reduced expression of MBD2 was detected in HCCs, and the expression of MeCP2 was particularly reduced in HCCs with portal vein involvement. These data suggest that overexpression of DNMT1 and DNMT3a, DNA hypermethylation on CpG islands, and DNA hypomethylation on pericentromeric satellite regions are early events during hepatocarci- Aberrant DNA cytosine methylation is one of the most consistent epigenetic changes in human cancers. 1 Generally, the overall DNA methylation level is lower in cancer cells than in normal cells. 2 However, some loci tend to show increased DNA methylation in cancer cells, 3-6 whereas others are often hypomethylated in human cancers. 7 DNA methylation may play roles in carcinogenesis by virtue of 3 mechanisms: 1) DNA cytosine methylation facilitates gene mutation, as 5-methylcytosine is deaminated to thymine 8 ; 2) aberrant DNA methylation may be associated with allelic loss 3-7,9-11 ; and 3) DNA methylation occurs frequently in CpG islands near regulatory regions of genes and affects the transcription of specific genes. 1,12,13 Recently, 2 types of DNA methylation were described; methylation of CpG islands in a cancer-specific manner (type C methylation) differs from age-dependent methylation (type A methylation). 14 CpG islands of the p16 and hMLH1 genes and the methylated in tumor (MINT) 1, 2, 12, 25, and 31 clones show type C methylation, 14 although the genes whose expression were regulated by MINT clones were not identified. A high level of type C methylation in human cancer has been referred to as the CpG island methylator phenotype (CIMP). 14,15 With respect to hepatocarcinogenesis, we reported previously that aberrant DNA methylation on chromosome 16, a hot spot for loss of heterozygosity (LOH) in hepatocellular carcinomas (HCCs), is observed frequently in chroni...

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Recognition sequences of restriction endonucleases and methylases — a review

Cited by 116 publications

References 274 publications

Restriction endonuclease activity induced by PBCV-1 virus infection of a Chlorella-like green alga.

Restriction endonuclease activity induced by PBCV-1 virus infection of a Chlorella-like green alga.

Characterization of the prolate-headed lactococcal bacteriophage OvML3: location of the lysin gene and its DNA homology with other prolate-headed phages

Expression of mRNA for DNA methyltransferases and methyl-CpG–binding proteins and DNA methylation status on CpG islands and pericentromeric satellite regions during human hepatocarcinogenesis

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