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Kroll J, Klinter S, Schneider C, Voss I, Steinbüchel A. Plasmid addiction systems: perspectives and applications in biotechnology. Microb Biotechnol 2010; 3:634-57. [PMID: 21255361 PMCID: PMC3815339 DOI: 10.1111/j.1751-7915.2010.00170.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 02/17/2010] [Indexed: 11/26/2022] Open
Abstract
Biotechnical production processes often operate with plasmid-based expression systems in well-established prokaryotic and eukaryotic hosts such as Escherichia coli or Saccharomyces cerevisiae, respectively. Genetically engineered organisms produce important chemicals, biopolymers, biofuels and high-value proteins like insulin. In those bioprocesses plasmids in recombinant hosts have an essential impact on productivity. Plasmid-free cells lead to losses in the entire product recovery and decrease the profitability of the whole process. Use of antibiotics in industrial fermentations is not an applicable option to maintain plasmid stability. Especially in pharmaceutical or GMP-based fermentation processes, deployed antibiotics must be inactivated and removed. Several plasmid addiction systems (PAS) were described in the literature. However, not every system has reached a full applicable state. This review compares most known addiction systems and is focusing on biotechnical applications.
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Affiliation(s)
- Jens Kroll
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, D-48149 Münster, Germany
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Affiliation(s)
- R J Roberts
- Cold Spring Harbor Laboratory, New York, NY 11724
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Raleigh EA, Wilson G. Escherichia coli K-12 restricts DNA containing 5-methylcytosine. Proc Natl Acad Sci U S A 1986; 83:9070-4. [PMID: 3024165 PMCID: PMC387076 DOI: 10.1073/pnas.83.23.9070] [Citation(s) in RCA: 225] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We have observed that plasmids containing certain cloned modification methylase genes of type II restriction-modification systems cannot be transformed into many laboratory strains of Escherichia coli K-12. The investigation of this phenomenon, reported here, has revealed (i) DNA containing 5-methylcytosine is biologically restricted by these strains, while DNA containing 6-methyladenine is not; (ii) restriction is due to two genetically distinct systems that differ in their sequence specificities, which we have named mcrA and mcrB (for modified cytosine restriction). Since 5-methylcytosine containing DNA is widespread in nature, the Mcr systems probably have a broad biological role. Mcr restriction may seriously interfere with molecular cloning of 5-methylcytosine-containing foreign DNAs. The Mcr phenotypes of some commonly used strains of E. coli K-12 are reported.
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Abstract
The properties and sources of all known restriction endonucleases and methylases are listed. The enzymes are cross-indexed (Table I), classified according to their recognition sequence homologies (Table II), and characterized within Table II by the cleavage and methylation positions, the number of recognition sites on the double-stranded DNA of the bacteriophages lambda, phi X174 and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and pBR328, and the microorganisms from which they originate. Other tabulated properties of the restriction endonucleases include relaxed specificities (integrated into Table II), the structure of the generated fragment ends (Table III), and the sensitivity to different kinds of DNA methylation (Table V). In Table IV the conversion of two- and four-base 5'-protruding ends into new recognition sequences is compiled which is obtained by the fill-in reaction with Klenow fragment of the Escherichia coli DNA polymerase I or additional nuclease S1 treatment followed by ligation of the modified fragment termini [P3]. Interconversion of restriction sites generates novel cloning sites without the need of linkers. This should improve the flexibility of genetic engineering experiments. Table VI classifies the restriction methylases according to the nature of the methylated base(s) within their recognition sequences. This table also comprises restriction endonucleases which are known to be inhibited or activated by the modified nucleotides. The detailed sequences of those overlapping restriction sites are also included which become resistant to cleavage after the sequential action of corresponding restriction methylases and endonucleases [N11, M21]. By this approach large DNA fragments can be generated which is helpful in the construction of genomic libraries. The data given in both Tables IV and VI allow the design of novel sequence specificities. These procedures complement the creation of universal cleavage specificities applying class IIS enzymes and bivalent DNA adapter molecules [P17, S82].
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Kessler C, Neumaier PS, Wolf W. Recognition sequences of restriction endonucleases and methylases--a review. Gene 1985; 33:1-102. [PMID: 2985469 DOI: 10.1016/0378-1119(85)90119-2] [Citation(s) in RCA: 104] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The properties and sources of all known endonucleases and methylases acting site-specifically on DNA are listed. The enzymes are crossindexed (Table I), classified according to homologies within their recognition sequences (Table II), and characterized within Table II by the cleavage and methylation positions, the number of recognition sites on the DNA of the bacteriophages lambda, phi X174 and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and pBR328 and the microorganisms from which they originate. Other tabulated properties of the restriction endonucleases include relaxed specificities (Table III), the structure of the restriction fragment ends (Table IV), and the sensitivity to different kinds of DNA methylation (Table V). Table VI classifies the methylases according to the nature of the methylated base(s) within their recognition sequences. This table also comprises those restriction endonucleases, which are known to be inhibited by the modified nucleotides. Furthermore, this review includes a restriction map of bacteriophage lambda DNA based on sequence data. Table VII lists the exact nucleotide positions of the cleavage sites, the length of the generated fragments ordered according to size, and the effects of the Escherichia coli dam- and dcmI-coded methylases M X Eco dam and M X Eco dcmI on the particular recognition sites.
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Roberts RJ. Restriction and modification enzymes and their recognition sequences. Nucleic Acids Res 1985; 13 Suppl:r165-200. [PMID: 2987885 PMCID: PMC320508 DOI: 10.1093/nar/13.suppl.r165] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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Cosstick R, McLaughlin LW, Eckstein F. Fluorescent labelling of tRNA and oligodeoxynucleotides using T4 RNA ligase. Nucleic Acids Res 1984; 12:1791-810. [PMID: 6366740 PMCID: PMC318621 DOI: 10.1093/nar/12.4.1791] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
3'-O-(5'-phosphoryldeoxycytidyl) phosphorothioate and fluorescent 3'-O-(5'-phosphoryldeoxycytidyl) S-bimane phosphorothioate can be ligated to tRNA by T4 RNA ligase. They are also efficient donors for the enzymatic ligation to oligodeoxynucleotides bearing a 3'-cytidine terminus. Cytidine 3',5'-bisphosphate is also a substrate for the ligation reaction with DNA restriction fragments with a 3'-terminate cytidylic acid residue. Oligo- and polynucleotides with a 3'-phosphorothioate group react readily with electrophiles as exemplified by the reaction with monobromobimane.
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Khosaka T, Kiwaki M, Rak B. Two site-specific endonucleases BinSI and BinSII from Bifidobacterium infantis. FEBS Lett 1983; 163:170-4. [PMID: 6315484 DOI: 10.1016/0014-5793(83)80812-6] [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: 01/19/2023]
Abstract
Two site-specific endonucleases, BinSI and BinSII, were isolated from Bifidobacterium infantis S76e. BinSI was found to be an isoschizomer of EcoRII, while BinSII was shown to have the same sequence and cutting specificity as BbeI, 5'-GGCGC decreases C-3'. Both BinSII- and BbeI-generated DNA fragments could be ligated with HaeII-generated DNA fragments.
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Roychoudhury R, Lam A. Isolation of a new plasmid pIRL19: its use in construction of small vectors and detection of specific sequence in a foreign DNA. Gene 1983; 25:161-6. [PMID: 6319230 DOI: 10.1016/0378-1119(83)90179-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A new plasmid, pIRL19, was constructed by ligating a 1875-bp HaeII fragment carrying the ampicillin-resistance (Apr) gene to a 370-bp HaeII fragment containing the replication origin of the plasmid pBR322. The plasmid essentially contains only the basic replicator and the Apr gene. This basic replicator provides a valuable initial building block for in vitro construction of other very small vectors with antibiotic-resistance determinants. To illustrate this potential, we have transferred the chloramphenicol-resistance (Cmr) gene and a part of the Apr gene from the plasmid pBR329 into pIRL19 such that the new plasmid pIRL20 acquired the Cmr gene and maintained the integrity of its Apr structural gene.
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Roberts RJ. Restriction and modification enzymes and their recognition sequences. Nucleic Acids Res 1982; 10:r117-44. [PMID: 6280143 PMCID: PMC320569 DOI: 10.1093/nar/10.5.1770] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Khosaka T, Sakurai T, Takahashi H, Saito H. A new site-specific endonuclease Bbei from Bifidobacterium breve. Gene X 1982; 17:117-22. [PMID: 6282709 DOI: 10.1016/0378-1119(82)90063-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Roberts RJ. Restriction and modification enzymes and their recognition sequences. Nucleic Acids Res 1981; 9:r75-96. [PMID: 6259615 PMCID: PMC326683 DOI: 10.1093/nar/9.1.213-c] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Abstract
Cordycepin-5'-triphosphate (3'-deoxyadenosine-5'-triphosphate) can be incorporated into the 3'-ends of DNA fragments using terminal deoxynucleotidyl transferase from calf thymus (Bollum, 1974). Because cordycepin-5'-monophosphate lacks a 3'-OH group, only a single residue is incorporated. Furthermore, DNA molecules that contain cordycepin-5'-monophosphate at their 3'-ends become resistant to hydrolysis by exonucleases that require free 3'-OH ends. As an alternative to 5'-end labeling of complementary DNA strands, we have used [32P]cordycepin-5'-triphosphate labeling of 3'-ends to confirm the nucleotide sequence of a HhaI-endonuclease-generated pTU4-plasmid DNA fragment that contains several hot spots for insertions of the transposable genetic element Tn3. 3'-End labeling with [32P] cordycepin-5'-triphosphate has also proved useful in determining the sequence of the pTU4 DNA in the vicinity of a strategically located SstII endonuclease cleavage site in the replication region of the plasmid.
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Roberts RJ. Restriction and modification enzymes and their recognition sequences. Nucleic Acids Res 1980; 8:r63-r80. [PMID: 6243774 PMCID: PMC327257 DOI: 10.1093/nar/8.1.197-d] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Shinomiya T, Sato S. A spite specific endonuclease from thermus thermophilus 111, Tth111I. Nucleic Acids Res 1980; 8:43-56. [PMID: 6243779 PMCID: PMC327241 DOI: 10.1093/nar/8.1.43] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A site specific endonuclease with novel specificity has been isolated from Thermus thermophilus strain 111 and named Tth111I. Tth111I cleaves lambda DNA into three fragments of 23.5, 25.7 and 50.8% of the total length, and ColE1 DNA into two fragments of nearly equal length. The sequences around Tth111I cleavage sites of ColE1 and lambda DNA were determined by the Maxam and Gilbert method and the two dimensional mapping method. The results suggest that Tth111I recognizes the DNA sequence (formula: see text) and cleaves the site as indicated by the arrows. Assuming that the first T.A pair in the sequence can be replaced for any base pair, the Tth111I recognition sequence has the symmetry with the two-fold axis as most type II restriction endonucleases do.
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Tu CP, Cohen SN. Translocation specificity of the Tn3 element: characterization of sites of multiple insertions. Cell 1980; 19:151-60. [PMID: 6244100 DOI: 10.1016/0092-8674(80)90396-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
247 independent events involving insertion of the TN3 transposable element into a 4 kb constructed plasmid (pTU4) of partially known DNA sequence were studied by restriction endonuclease mapping, and 65 of these insertion sites were examined further by DNA sequence analysis. Our results show that the previously proposed regional specificity for Tn3 insertion is associated with a strong preference for AT-rich segments as insertion sites. Moreover, multiple insertions of the Tn3 occurred at certain AT-rich nucleotide positions, and 23 of 26 independent insertion events at a single nucleotide position were found to be in the same orientation. A region of the recipient plasmid showing major homology with the terminal 18 bp of Tn3 was identified in the vicinity of an 11 nucleotide segment that included three insertional hot spots and 36 independent insertions. Our results indicate that the site and orientation of insertion of Tn3 are at least partly determined by the primary nucleotide sequence of the recipient genome, and suggest that insertional hot spots may result from the combined effects of AT richness plus homology of the recipient genome with the terminal sequences of Tn3.
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Roychoudhury R, Wu R. Terminal transferase-catalyzed addition of nucleotides to the 3' termini of DNA. Methods Enzymol 1980; 65:43-62. [PMID: 6246363 DOI: 10.1016/s0076-6879(80)65009-5] [Citation(s) in RCA: 130] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Berkner K, Folk W. The effects of substituted pyrimidines in DNAs on cleavage by sequence-specific endonucleases. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(17)30256-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Berkner K, Folk W. Quantitation of the various termini generated by type II restriction endonucleases using the polynucleotide kinase exchange reaction. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(17)30257-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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de Waard A, Korsuize J, van Beveren CP, Maat J. A new sequence-specific endonuclease from Anabaena cylindrica. FEBS Lett 1978; 96:106-10. [PMID: 103749 DOI: 10.1016/0014-5793(78)81072-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Ysebaert M, van de Voorde A, Fiers W. Nucleotide sequence of the simian virus 40 HindII + III restriction fragment D and the total amino acid sequence of the late proteins VP2 and VP3. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 91:431-9. [PMID: 215403 DOI: 10.1111/j.1432-1033.1978.tb12695.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Brown KD, Bennett GN, Lee F, Schweingruber ME, Yanofsky C. RNA polymerase interaction at the promoter--operator region of the tryptophan operon of Escherichia coli and Salmonella typhimurium. J Mol Biol 1978; 121:153-77. [PMID: 351193 DOI: 10.1016/s0022-2836(78)80003-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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de la Maza LM, Carter BJ. Adeno-associated virus DNA structure. Restriction endonuclease maps and arrangement of terminal sequences. Virology 1977; 82:409-30. [PMID: 919346 DOI: 10.1016/0042-6822(77)90016-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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