1
|
Pristas P, Piknova M. Underrepresentation of short palindromes in Selenomonas ruminantium DNA: evidence for horizontal gene transfer of restriction and modification systems? Can J Microbiol 2005; 51:315-8. [PMID: 15980893 DOI: 10.1139/w05-004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molecular analysis of isolates of the rumen bacterium Selenomonas ruminantium revealed a high variety and frequency of site-specific (restriction) endonucleases. While all known S. ruminantium restriction and modification systems recognize hexanucleotide sequences only, consistently low counts of both 6-bp and 4-bp palindromes were found in DNA sequences of S. ruminantium. Statistical analysis indicated that there is some correlation between the degree of underrepresentation of tetranucleotide words and the number of known restriction endonucleases for a given sequence. Control analysis showed the same correlation in lambda DNA but not in human adenovirus DNA. Based on the data presented, it could be proposed that there is a much higher historical occurrence of restriction and modification systems in S. ruminantium and (or) frequent horizontal gene transfer of restriction and modification gene complexes.
Collapse
Affiliation(s)
- Peter Pristas
- Institute of Animal Physiology, Slovak Academy of Sciences, Soltesovej 4-6, 04001 Kosice, Slovak Republic.
| | | |
Collapse
|
2
|
Bilcock DT, Halford SE. DNA restriction dependent on two recognition sites: activities of the SfiI restriction-modification system in Escherichia coli. Mol Microbiol 1999; 31:1243-54. [PMID: 10096090 DOI: 10.1046/j.1365-2958.1999.01266.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In contrast to many type II restriction enzymes, dimeric proteins that cleave DNA at individual recognition sites 4-6 bp long, the SfiI endonuclease is a tetrameric protein that binds to two copies of an elongated sequence before cutting the DNA at both sites. The mode of action of the SfiI endonuclease thus seems more appropriate for DNA rearrangements than for restriction. To elucidate its biological function, strains of Escherichia coli expressing the SfiI restriction-modification system were transformed with plasmids carrying SfiI sites. The SfiI system often failed to restrict the survival of a plasmid with one SfiI site, but plasmids with two or more sites were restricted efficiently. Plasmids containing methylated SfI sites were not restricted. No rearrangements of the plasmids carrying SfiI sites were detected among the transformants. Hence, provided the target DNA contains at least two recognition sites, SfiI displays all of the hallmarks of a restriction-modification system as opposed to a recombination system in E. coli cells. The properties of the system in vivo match those of the enzyme in vitro. For both restriction in vivo and DNA cleavage in vitro, SfiI operates best with two recognition sites on the same DNA.
Collapse
Affiliation(s)
- D T Bilcock
- Department of Biochemistry, School of Medical Sciences, University of Bristol, UK
| | | |
Collapse
|
3
|
Abstract
We determined the genomic structure of the gene encoding human DNA methyltransferase (DNA MTase). Six overlapping human genomic DNA clones which include all of the known cDNA sequence were isolated. Analysis of these clones demonstrates that the human DNA MTase gene consists of at least 40 exons and 39 introns spanning a distance of 60 kilobases. Elucidation of the chromosomal organization of the human DNA MTase gene provides the template for future structure-function analysis of the properties of mammalian DNA MTase.
Collapse
Affiliation(s)
- S Ramchandani
- Department of Pharmacology and Therapeutics, McGill University, Montreal, PQ, Canada
| | | | | |
Collapse
|
4
|
Carlson K, Kosturko LD, Nyström AC. Short-range and long-range context effects on coliphage T4 endonuclease II-dependent restriction. J Bacteriol 1996; 178:6419-26. [PMID: 8932296 PMCID: PMC178526 DOI: 10.1128/jb.178.22.6419-6426.1996] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Synthetic sites inserted into a plasmid were used to analyze the sequence requirements for in vivo DNA cleavage dependent on bacteriophage T4 endonuclease II. A 16-bp variable sequence surrounding the cleavage site was sufficient for cleavage, although context both within and around this sequence influenced cleavage efficiency. The most efficiently cleaved sites matched the sequence CGRCCGCNTTGGCNGC, in which the strongly conserved bases to the left were essential for cleavage. The less-conserved bases in the center and in the right half determined cleavage efficiency in a manner not directly correlated with the apparent base preference at each position; a sequence carrying, in each of the 16 positions, the base most preferred in natural sites in pBR322 was cleaved infrequently. This, along with the effects of substitutions at one or two of the less-conserved positions, suggests that several combinations of bases can fulfill the requirements for recognition of the right part of this sequence. The replacements that improve cleavage frequency are predicted to influence helical twist and roll, suggesting that recognition of sequence-dependent DNA structure and recognition of specific bases are both important. Upon introduction of a synthetic site, cleavage at natural sites within 800 to 1,500 bp from the synthetic site was significantly reduced. This suggests that the enzyme may engage more DNA than its cleavage site and cleaves the best site within this region. Cleavage frequency at sites which do not conform closely to the consensus is, therefore, highly context dependent. Models and possible biological implications of these findings are discussed.
Collapse
Affiliation(s)
- K Carlson
- Department of Microbiology, University of Uppsala Biomedical Center, Sweden.
| | | | | |
Collapse
|
5
|
Carlson K, Krabbe M, Nyström A, Kosturko L. DNA determinants of restriction. Bacteriophage T4 endonuclease II-dependent cleavage of plasmid DNA in vivo. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)52959-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
6
|
Wenzel R, Pirkl E, Herrmann R. Construction of an EcoRI restriction map of Mycoplasma pneumoniae and localization of selected genes. J Bacteriol 1992; 174:7289-96. [PMID: 1429453 PMCID: PMC207423 DOI: 10.1128/jb.174.22.7289-7296.1992] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A restriction map of the genome of Mycoplasma pneumoniae, a small human pathogenic bacterium, was constructed by means of an ordered cosmid library which spans the complete bacterial chromosome. The positions of 143 endonuclease EcoRI restriction fragments were determined and aligned with the physical map. In addition, restriction sites for the rare-cutting enzymes XhoI (25 sites), ApaI (13 sites), NotI (2 sites), and SfiI (2 sites) were included. The resulting map consists of 185 restriction sites, has a mean resolution of 4.4 kbp, and predicts a genome size of 809 kbp. In addition, several genes were identified and mapped to their respective genomic EcoRI restriction fragments.
Collapse
Affiliation(s)
- R Wenzel
- ZMBH, University of Heidelberg, Germany
| | | | | |
Collapse
|
7
|
Lechner M, Frey B, Laue F, Anton-Botella J, Smith CL, Ankenbauer W, Schmitz GG. SwaI, a unique restriction endonuclease from Staphylococcus warneri, which recognizes 5'-ATTTAAAT-3'. Nucleic Acids Res 1992; 20:2293-6. [PMID: 1594448 PMCID: PMC312344 DOI: 10.1093/nar/20.9.2293] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A novel class-II restriction endonuclease designated SwaI was purified from Staphylococcus warneri. This enzyme cleaves adenovirus 2 DNA, SV40 DNA and M13mp7 at one site each, but does not cleave lambda, PhiX174, pBR322 or pBR328 DNA. SwaI recognizes the octanucleotide sequence 5'-ATTTAAAT-3', cleaving in the center of the recognition sequence creating blunt ended DNA fragments. SwaI was used to digest chromosomal DNA from various microorganisms and human cells.
Collapse
Affiliation(s)
- M Lechner
- Boehringer Mannheim GmbH, Biochemical Research Center, Penzberg, Germany
| | | | | | | | | | | | | |
Collapse
|
8
|
Waite-Rees PA, Keating CJ, Moran LS, Slatko BE, Hornstra LJ, Benner JS. Characterization and expression of the Escherichia coli Mrr restriction system. J Bacteriol 1991; 173:5207-19. [PMID: 1650347 PMCID: PMC208215 DOI: 10.1128/jb.173.16.5207-5219.1991] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The mrr gene of Escherichia coli K-12 is involved in the acceptance of foreign DNA which is modified. The introduction of plasmids carrying the HincII, HpaI, and TaqI R and M genes is severely restricted in E. coli strains that are Mrr+. A 2-kb EcoRI fragment from the plasmid pBg3 (B. Sain and N. E. Murray, Mol. Gen. Genet. 180:35-46, 1980) was cloned. The resulting plasmid restores Mrr function to mrr strains of E. coli. The boundaries of the mrr gene were determined from an analysis of subclones, and plasmids with a functional mrr gene produce a polypeptide of 33.5 kDa. The nucleotide sequence of the entire fragment was determined; in addition to mrr, it includes two open reading frames, one of which encodes part of the hsdR. By using Southern blot analysis, E. coli RR1 and HB101 were found to lack the region containing mrr. The acceptance of various cloned methylases in E. coli containing the cloned mrr gene was tested. Plasmid constructs containing the AccI, CviRI, HincII, Hinfl (HhaII), HpaI, NlaIII, PstI, and TaqI N6-adenine methylases and SssI and HhaI C5-cytosine methylases were found to be restricted. Plasmid constructs containing 16 other adenine methylases and 12 cytosine methylases were not restricted. No simple consensus sequence causing restriction has been determined. The Mrr protein has been overproduced, an antibody has been prepared, and the expression of mrr under various conditions has been examined. The use of mrr strains of E. coli is suggested for the cloning of N6-adenine and C5-cytosine methyl-containing DNA.
Collapse
|
9
|
Abstract
A physical map of the Methanococcus voltae chromosome was constructed on the basis of restriction mapping and cross-hybridization experiments, employing total and partial digests obtained with rarely cutting restriction enzymes. On the basis of the sum of the fragment sizes of digests with seven enzymes the chromosome length was calculated to be approximately 1900 kb. The derived map is circular. Hybridization of gene probes to mapped restriction fragments has led to a genetic map of genes for structural RNAs as well as proteins, including enzymes involved in the methanogenic pathway.
Collapse
Affiliation(s)
- J Sitzmann
- Molekulargenetik, Fachbereich Biologie, Philipps-Universität, Marburg, Germany
| | | |
Collapse
|
10
|
Gachechiladze KK, Balardshishvili NS, Adamia RS, Chanishvili TG, Krüger DH. Host-controlled modification and restriction as a criterion of evaluating the therapeutical potential of Pseudomonas phage. J Basic Microbiol 1991; 31:101-6. [PMID: 1880713 DOI: 10.1002/jobm.3620310206] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The recently isolated phages phi ST3 and phi ST1 were compared as to their lysis behaviour in about 100 different P. aeruginosa strains. The growth of phi ST3 varies greatly in different host strains. We demonstrated one case of "non-classical", host-dependent modification and restriction. Here the capability to adsorb, and consequently to reproduce in a given host strain differs, depending on which modification the phage acquired in its former host. The DNA-containing phage phi ST1 displays stable lysis properties in the majority of the host strains. This makes phi ST1 a candidate for therapeutic phage preparations. One of the reasons for stable lysis properties is the apparent selection against recognition sites of restriction enzymes in its genome.
Collapse
Affiliation(s)
- K K Gachechiladze
- Institute of Sera and Vaccines, Scientific-Industrial Union Bacteriophages, Georgia, USSR
| | | | | | | | | |
Collapse
|
11
|
Kotani H, Nomura Y, Kawashima Y, Sagawa H, Takagi M, Kita A, Ito H, Kato I. Sse8387I, a new type-II restriction endonuclease that recognizes the octanucleotide sequence 5'-CCTGCAGG-3'. Nucleic Acids Res 1990; 18:5637-40. [PMID: 2170941 PMCID: PMC332294 DOI: 10.1093/nar/18.19.5637] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A type II restriction endonuclease designated Sse8387I was partially purified from Streptomyces sp. 8387. This enzyme cleaved adenovirus 2 DNA at three sites, lambda phage DNA at five sites, and pUC18 and M13mp18 RF DNA at one site each, but did not cleave the DNAs from pBR322, SV40, or phi X174. Sse8387I recognized the octanucleotide sequence 5'-CCTGCA decreases GG-3', cleaving where shown by the arrow. Sse8387I is the first restriction endonuclease to be reported that recognizes an octanucleotide sequence consisting of all four nucleotides, G, A, T, and C. The frequency of occurrence of Sse8387I sites within sequenced regions of primate genomes was 2.4 times that of NotI sites.
Collapse
Affiliation(s)
- H Kotani
- Bioproducts Development and Research Center, Takara Shuzo Co., Ltd., Shiga, Japan
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Nelson JM, Miceli SM, Lechevalier MP, Roberts RJ. FseI, a new type II restriction endonuclease that recognizes the octanucleotide sequence 5' GGCCGGCC 3'. Nucleic Acids Res 1990; 18:2061-4. [PMID: 2159636 PMCID: PMC330683 DOI: 10.1093/nar/18.8.2061] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A Type II restriction endonuclease, designated FseI, has been partially purified from a Frankia species (NRRL 18528). This enzyme cleaves Adenovirus 2 DNA at three sites, but does not cleave the DNAs from bacteriophages lambda, T7, and phi X174, the animal virus SV40, pUC18 and pBR322. FseI recognizes the octanucleotide sequence 5' GGCCGG decreases CC 3' and cleaves as indicated by the arrow. The frequency of occurrence of FseI sites within sequenced regions of the human genome is similar to that for NotI sites.
Collapse
|
13
|
Stephenson FH, Ballard BT, Boyer HW, Rosenberg JM, Greene PJ. Comparison of the nucleotide and amino acid sequences of the RsrI and EcoRI restriction endonucleases. Gene 1989; 85:1-13. [PMID: 2695392 DOI: 10.1016/0378-1119(89)90458-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The RsrI endonuclease, a type-II restriction endonuclease (ENase) found in Rhodobacter sphaeroides, is an isoschizomer of the EcoRI ENase. A clone containing an 11-kb BamHI fragment was isolated from an R. sphaeroides genomic DNA library by hybridization with synthetic oligodeoxyribonucleotide probes based on the N-terminal amino acid (aa) sequence of RsrI. Extracts of E. coli containing a subclone of the 11-kb fragment display RsrI activity. Nucleotide sequence analysis reveals an 831-bp open reading frame encoding a polypeptide of 277 aa. A 50% identity exists within a 266-aa overlap between the deduced aa sequences of RsrI and EcoRI. Regions of 75-100% aa sequence identity correspond to key structural and functional regions of EcoRI. The type-II ENases have many common properties, and a common origin might have been expected. Nevertheless, this is the first demonstration of aa sequence similarity between ENases produced by different organisms.
Collapse
Affiliation(s)
- F H Stephenson
- Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0554
| | | | | | | | | |
Collapse
|
14
|
Heidmann S, Seifert W, Kessler C, Domdey H. Cloning, characterization and heterologous expression of the SmaI restriction-modification system. Nucleic Acids Res 1989; 17:9783-96. [PMID: 2690008 PMCID: PMC335213 DOI: 10.1093/nar/17.23.9783] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The genes coding for the class-II Serratia marcescens restriction-modification system have been cloned and expressed in E. coli. Recombinant clones, restricted incoming phage only poorly; the recombinant plasmids, however, became fully modified in vivo, i.e. completely resistant against digestion with R.SmaI. The determined nucleotide sequence of the cloned system revealed three open reading frames with lengths of 252 bp, 741 bp, and 876 bp. Through various deletion experiments and an insertion-mutation experiment the 876 bp open reading frame could be assigned to the SmaI DNA modification enzyme and the 741 bp open reading frame to the SmaI restriction endonuclease. Mapping of the transcription start sites of the genes revealed that the SmaI endonuclease is transcribed as polycistronic mRNA together with a 252 bp long preceding open reading frame of unknown function. No homology was found when comparing the amino acid sequence of M.SmaI with the published sequences of m5C-specific DNA modification methyltransferases. On the other hand, a stretch of 14 amino acids in the C-proximal region of M.SmaI shows a significant homology to the C-proximal amino acid sequences of the N6A-methyltransferases M.HinfI and M.DpnIIA and the N4C-methyltransferase M.PvuII.
Collapse
Affiliation(s)
- S Heidmann
- Laboratorium für Molekulare Biologie, Genzentrum, der Ludwig-Maximilians-Universität München, FRG
| | | | | | | |
Collapse
|
15
|
Verhasselt P, Poncelet F, Vits K, Van Gool A, Vanderleyden J. Cloning and expression of a Clostridium acetobutylicum alpha-amylase gene in Escherichia coli. FEMS Microbiol Lett 1989; 50:135-40. [PMID: 2661316 DOI: 10.1111/j.1574-6968.1989.tb03097.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A gene library of Clostridium acetobutylicum ATCC824 was constructed in the plasmid vector pEcoR251. The library was tested for the presence of starch hydrolyzing clones. One clone in which the recombinant plasmid, pVP101, conferred alpha-amylase activity to the Escherichia coli host cell, was detected. The gene is carried on a 3.45-kbp BglII restriction fragment. A detailed physical map of pVP101 is presented.
Collapse
Affiliation(s)
- P Verhasselt
- F.A. Janssens Memorial Laboratory of Genetics, University of Leuven, Heverlee, Belgium
| | | | | | | | | |
Collapse
|
16
|
Weil MD, McClelland M. Enzymatic cleavage of a bacterial genome at a 10-base-pair recognition site. Proc Natl Acad Sci U S A 1989; 86:51-5. [PMID: 2536159 PMCID: PMC286401 DOI: 10.1073/pnas.86.1.51] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The circular genome of Staphylococcus aureus was cut into two fragments by a simple enzymatic method that cleaves a 10-base-pair site. The recognition sequence, A-T-C-G-mA decreases T-C-G-mA-T, was created by the combined use of the methylase M.Cla I (A-T-C-G-mA-T) and the restriction endonuclease Dpn I (G-mA decreases T-C). This technique is insensitive to CpG methylation and in human DNA is predicted to produce fragments that, on average, are greater than five million base pairs. The ability to create such long pieces of DNA should facilitate mapping of large, complex chromosomes.
Collapse
Affiliation(s)
- M D Weil
- Department of Biochemistry, University of Chicago, IL 60637
| | | |
Collapse
|