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Lyra C, Halme T, Torsti AM, Tenkanen T, Sivonen K. Site-specific restriction endonucleases in cyanobacteria. J Appl Microbiol 2000; 89:979-91. [PMID: 11123471 DOI: 10.1046/j.1365-2672.2000.01206.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIM Planktic cyanobacteria were screened for endodeoxyribonucleases. Principal component analysis (PCA) was employed to demonstrate a potential relationship between certain enzymes and a group of cyanobacteria. The data were obtained from a data bank and this study. METHODS AND RESULTS Enzymes were partially purified using column chromatography. Anabaena strains contained Asp83/1I (5'-TTCGAA-3'), Asp83/1II (5'-GGCC-3'), Asp90I (5'-ACRYGT-3') and five isoschizomeric enzymes (5'-ATCGAT-3'). Aphanizomenon and Microcystis strains contained ApcTR183I (5'-TGCGCA-3') and Msp199I (5'-CCGG-3'), respectively. Planktothrix strains possessed Psc2I (5'-GAANNNNTTC-3'), Psc27I and Psc28I (5'-TTCGAA-3'). PCA showed that the most common cyanobacterial endonuclease types were AvaII, AvaI and AsuII. CONCLUSIONS All planktic cyanobacteria studied contained restriction endonucleases. The defined restriction endonucleases were isoschizomers of known enzymes. The Nostoc and the Spirulina genera had an association, while the majority of the genera had no association with certain endonuclease type(s). SIGNIFICANCE AND IMPACT OF THE STUDY The defined enzymes in this study and the estimated trend in the endonuclease type distribution allow more efficient avoidance of cyanobacterial restriction barriers.
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Affiliation(s)
- C Lyra
- Department of Applied Chemistry and Microbiology, Helsinki University, and Finnzymes Oy, Espoo, Finland
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2
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Fiore MF, Moon DH, Tsai SM, Lee H, Trevors JT. Miniprep DNA isolation from unicellular and filamentous cyanobacteria. J Microbiol Methods 2000; 39:159-69. [PMID: 10576706 DOI: 10.1016/s0167-7012(99)00110-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A rapid miniprep method for isolation of DNA from 12 strains of cyanobacteria belonging to groups I, III, IV and V is described. The protocol is a modification of the methods of Boyle and Lew [Boyle, J.S., Lew, A.M., 1995. An inexpensive alternative to glassmilk for DNA purification. Trends Genet. 11, 8] and the cetyltrimethyl ammonium bromide (CTAB) extraction method of Sahgai-Maroof et al. [Sahgai-Maroof, M.A., Soliman, K.M., Jorgensen, R.A., Allard, R.W., 1984. Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location and population dynamics. Proc. Natl. Acad. Sci. USA 81, 8014-80181. The new method is especially useful for obtaining cyanobacterial DNA from unicellular, filamentous and filamentous branched species. The method does not require phenol extraction and the product can be used directly for PCR amplification and restriction digestion.
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Affiliation(s)
- M F Fiore
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba SP, Brazil.
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3
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Kawata Y, Yano S, Thankappan AK, Daniel EC, Kojima H. Preparation of a genomic library using a TA vector. Prep Biochem Biotechnol 1999; 29:91-100. [PMID: 10069436 DOI: 10.1080/10826069908544696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
An efficient and simple method for constructing a genomic DNA library is presented using a TA cloning vector. It is based on sonication cleavage of genomic DNA, blunting of the fragment ends with mung bean nuclease, and addition of a single 3'-deoxyadenylate with Taq DNA polymerase, followed by ligation with a TA vector. This method is useful for improving the quality of genomic libraries for organisms whose genomic DNA is not well digested with restriction enzymes owing to the presence of polysaccharides and/or DNA methylation.
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Affiliation(s)
- Y Kawata
- Osaka National Research Institute, Agency of Industrial Science and Technology, Ikeda, Japan
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4
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Scharnagl M, Richter S, Hagemann M. The cyanobacterium Synechocystis sp. strain PCC 6803 expresses a DNA methyltransferase specific for the recognition sequence of the restriction endonuclease PvuI. J Bacteriol 1998; 180:4116-22. [PMID: 9696758 PMCID: PMC107406 DOI: 10.1128/jb.180.16.4116-4122.1998] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/1998] [Accepted: 05/30/1998] [Indexed: 11/20/2022] Open
Abstract
By use of restriction endonucleases, the DNA of the cyanobacterium Synechocystis sp. strain PCC 6803 was analyzed for DNA-specific methylation. Three different recognition sites of methyltransferases, a dam-like site including N6-methyladenosine and two other sites with methylcytosine, were identified, whereas no activities of restriction endonucleases could be detected in this strain. slr0214, a Synechocystis gene encoding a putative methyltransferase that shows significant similarities to C5-methylcytosine-synthesizing enzymes, was amplified by PCR and cloned for further characterization. Mutations in slr0214 were generated by the insertion of an aphII gene cassette. Analyses of chromosomal DNAs of such mutants demonstrated that the methylation pattern was changed. The recognition sequence of the methyltransferase was identified as 5'-CGATCG-3', corresponding to the recognition sequence of PvuI. The specific methyltransferase activity was significantly reduced in protein extracts obtained from mutant cells. Mutation of slr0214 also led to changed growth characteristics of the cells compared to wild-type cells. These alterations led to the conclusion that the methyltransferase Slr0214 might play a regulatory role in Synechocystis. The Slr0214 protein was also overexpressed in Escherichia coli, and the purified protein demonstrated methyltransferase activity and specificity for PvuI recognition sequences in vitro. We propose the designation M.Ssp6803I [corrected] (Synechocystis methyltransferase I) for the slr0214-encoded enzyme.
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Affiliation(s)
- M Scharnagl
- FB Biologie, Universität Rostock, D-18051 Rostock, Germany
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5
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Schyns G, Rippka R, Namane A, Campbell D, Herdman M, Houmard J. Prochlorothrix hollandica PCC 9006: genomic properties of an axenic representative of the chlorophyll a/b-containing oxyphotobacteria. Res Microbiol 1997; 148:345-54. [PMID: 9765813 DOI: 10.1016/s0923-2508(97)81590-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Prochlorothrix hollandica is an oxygenic photosynthetic prokaryote that differs from the cyanobacteria in having chlorophyll a/b-protein complexes instead of phycobilisomes as major light-harvesting antennae. We report the isolation and culturing of an axenic strain of P. hollandica, available from the Pasteur Culture Collection of Cyanobacteria as strain PCC 9006. The strain has a mean DNA base composition of 51.6 +/- 0.1 mol% G+C and a genomic complexity of 3.37 +/- 0.17 x 10(9) daltons (5,505 kb). A reiterated DNA sequence represents approximately 4.4% of the genome. Restriction enzyme isoschizomers with different sensitivities to base methylation were used to demonstrate that most A residues in the sequence GATC are methylated in P. hollandica DNA and that this methylation increases with culture age. Furthermore, some C residues are methylated, although the specificity of the C methylation system does not match that of well-characterized C methylases. Nucleotide analysis showed that up to approximately 3.5% of both dA and dC residues are methylated in P. hollandica DNA.
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Affiliation(s)
- G Schyns
- Unité de Physiologie microbienne (CNRS URA 1129), Institut Pasteur, Paris
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6
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Diversity of DNA methylation pattern and total DNA restriction pattern in symbiotic Nostoc. World J Microbiol Biotechnol 1996; 12:38-42. [DOI: 10.1007/bf00327797] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/09/1995] [Accepted: 08/09/1995] [Indexed: 11/26/2022]
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7
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Soper BW, Reddy KJ. Identification of a nuclease and host restriction-modification in the unicellular, aerobic nitrogen-fixing cyanobacterium Cyanothece sp. J Bacteriol 1994; 176:5565-70. [PMID: 8071241 PMCID: PMC196751 DOI: 10.1128/jb.176.17.5565-5570.1994] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
In the process of developing a gene transfer system for the marine, unicellular, nitrogen-fixing cyanobacterium Cyanothece sp. strain BH68K, two major restriction barriers have been identified. A cell wall-associated nuclease exhibited non-site-specific degradation of covalently closed circular and linear double-stranded DNA molecules, including Cyanothece sp. strain BH68K chromosomal DNA. The nuclease is easily released from intact cells by using water or buffer containing Triton X-100. Nuclease activity was undetectable in cell extracts prepared from water-washed cells. Comparison of the restriction endonuclease susceptibility of Cyanothece sp. strain BH68K DNA to that of Anabaena sp. strain PCC 7120 revealed that these organisms have a nearly identical pattern of restriction and therefore may contain similar systems for DNA methylation. Restriction by DpnI, MboI, and Sau3AI indicated the presence of adenine methylation. Cyanothece sp. strain BH68K cell extracts contain a type II restriction endonuclease, Csp68KI. The activity of Csp68KI was easily detected in cell extracts without extensive purification. Csp68KI is an isoschizomer of AvaII and recognizes the nucleotide sequence 5'-GG(A/T)CC-3'. Cleavage occurs between the guanosine nucleotides producing 3-bp 5' overhang ends.
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Affiliation(s)
- B W Soper
- Department of Biological Sciences, State University of New York-Binghamton 13902
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8
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Zimmerman WJ, Culley DE. Genetic variation at theapcAB,cpcAB,gvpA1, andnifH loci and in DNA methylation among N2-fixing cyanobacteria designatedNostoc punctiforme. MICROBIAL ECOLOGY 1991; 21:199-209. [PMID: 24194211 DOI: 10.1007/bf02539154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/1990] [Revised: 02/25/1991] [Indexed: 06/02/2023]
Abstract
Genetic similarity among cyanobacteria of a morphological subgroup ofNostoc was evaluated through a comparison of several specific genes and the extent of DNA methylation. Four of six cyanobacteria were originally cultured from facultative symbioses with higher plants (Gunnera andEncephalartos); these and one free-living isolate had been identified or reputed to beN. punctiforme. No consistent correlation to species or symbiotic history was found from DNA hybridizations to genes coding for phycocyanin (cpcAB), allophycocyanin (apcAB), gas vesicle protein (gvpA1), and dinitrogenase reductase (nifH). One gene (gvpC) was not present, andgvpA1 was a single-copy gene in all strains. The gas vesicle genes were concluded to be potentially useful for broadly characterizingNostoc or at least this subgroup. Incubations ofNostoc genomic DNA with 22 restriction endonucleases indicated a high degree of methylation and similarity of its methylated DNA to that of other heterocystous cyanobacteria. The genetic variation of theNostoc isolates was judged to reflect primarily different soil origins.
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Affiliation(s)
- W J Zimmerman
- Department of Natural Sciences, University of Michigan-Dearborn, 48128-1491, Dearborn, Michigan, USA
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9
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Zehr JP, Ohki K, Fujita Y, Landry D. Unique modification of adenine in genomic DNA of the marine cyanobacterium Trichodesmium sp. strain NIBB 1067. J Bacteriol 1991; 173:7059-62. [PMID: 1657876 PMCID: PMC209068 DOI: 10.1128/jb.173.21.7059-7062.1991] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The genomic DNA of the marine nonheterocystous nitrogen-fixing cyanobacterium Trichodesmium sp. strain NIBB 1067 was found to be highly resistant to DNA restriction endonucleases. The DNA was digested extensively by the restriction enzyme DpnI, which requires adenine methylation for activity. The DNA composition, determined by high-performance liquid chromatography (HPLC), was found to be 69% AT. Surprisingly, it was found that a modified adenine which was not methylated at the usual N6 position was present and made up 4.7 mol% of the nucleosides in Trichodesmium DNA (15 mol% of deoxyadenosine). In order for adenine residues to be modified at this many positions, there must be many modifying enzymes or at least one of the modifying enzymes must have a degenerate recognition site. The reason(s) for this extensive methylation has not yet been determined but may have implications for the ecological success of this microorganism in nature.
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Affiliation(s)
- J P Zehr
- Marine Sciences Research Center, State University of New York, Stony Brook 11794
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10
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Abstract
The complete type II modification methylase of Agmenellum quadruplicatum was cloned in Escherichia coli as an R.Sau3A fragment of approximately 4.5 kilobases. The coding sequence was contained in a stretch of 1,156 base pairs which was organized into two parallel, partly overlapping open reading frames of 248 and 139 codons. In vivo complementation experiments showed that the synthesis of both predicted peptides was required for full methylase activity. The amino acid sequences were considerably similar to regions of other deoxycytidylate methylases.
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Affiliation(s)
- C Karreman
- Sylvius Laboratories, Department of Medical Biochemistry, University of Leiden, The Netherlands
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11
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Bancroft I, Wolk CP, Oren EV. Physical and genetic maps of the genome of the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120. J Bacteriol 1989; 171:5940-8. [PMID: 2509424 PMCID: PMC210458 DOI: 10.1128/jb.171.11.5940-5948.1989] [Citation(s) in RCA: 91] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A restriction map of the chromosome of the cyanobacterium Anabaena sp. strain PCC 7120 was generated by the determination of the order of restriction fragments of the infrequently cleaving restriction endonucleases AvrII, SalI, and PstI. These restriction fragments were resolved by the pulsed homogeneous orthogonal field gel electrophoresis system of pulsed-field gel electrophoresis (I. Bancroft and C. P. Wolk, Nucleic Acids Res. 16:7405-7418, 1988). Other infrequently cutting restriction endonucleases (AhaII, Asp718, AsuII, BanII, BglII, BssHII, FspI, NcoI, NruI, SphI, SplI, SstII, and StuI) were identified that could prove useful for higher-resolution mapping. The chromosome was found to be 6.4 megabases in size and circular. Three apparently circular large plasmids (410, 190, and 110 kilobases) were also identified. A genetic map was constructed by hybridization with gene-specific probes. Genes encoding components of the photosynthetic electron transport chain were not within a single tight cluster.
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Affiliation(s)
- I Bancroft
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing 48824-1312
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12
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Douglas SE, Carr N. Examination of Genetic Relatedness of Marine
Synechococcus
spp. by Using Restriction Fragment Length Polymorphisms. Appl Environ Microbiol 1988; 54:3071-8. [PMID: 16347797 PMCID: PMC204429 DOI: 10.1128/aem.54.12.3071-3078.1988] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The relatedness of several marine
Synechococcus
spp. was estimated by DNA hybridization. Strains isolated from various geographical locations and representing a diversity of DNA base compositions and phycobiliprotein profiles were compared by restriction fragment length polymorphisms for a number of genes. DNAs from two marine red algae and a cryptomonad alga (which exhibit a phycobiliprotein composition similar to that of the marine
Synechococcus
spp.) and
Synechococcus
strain PCC6301 (
Anacystis nidulans
) were also included in the comparison. Strains WH8008, WH8018, and WH7805 were shown to be very similar to one another, as were strains WH7802 and WH7803. Strains WH8110 and WH5701 were clearly unrelated to any of the other strains, and no marine
Synechococcus
isolate showed any similarity to the freshwater
Synechococcus
strain PCC6301 or the eucaryotic algae. The method is relatively straightforward and sensitive and uses a variety of basic molecular biology techniques. Its utility in ascertaining the genetic relatedness and diversity of marine
Synechococcus
spp. and possible extension to field studies are discussed.
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Affiliation(s)
- S E Douglas
- National Research Council, 1411 Oxford Street, Halifax, Nova Scotia, Canada B3H 3ZI, and Department of Biological Sciences, University of Warwick, Coventry, England, CV4 7AL
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13
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Karreman C, de Waard A. Cloning and complete nucleotide sequences of the type II restriction-modification genes of Salmonella infantis. J Bacteriol 1988; 170:2527-32. [PMID: 2836359 PMCID: PMC211166 DOI: 10.1128/jb.170.6.2527-2532.1988] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The complete type II restriction-modification system of Salmonella infantis was cloned in Escherichia coli as an R . Sau3AI fragment of 3,430 base pairs. The clone was shown to express the restriction endonuclease as well as the modification methylase. The nucleotide sequence of the above fragment showed two open reading frames of 461 and 230 codons in tail-to-tail orientation. These were shown to represent the modification methylase M . SinI and the restriction endonuclease R . SinI, respectively. The methylase M . SinI amino acid sequence revealed a considerable similarity to those of other deoxycytidylate methylases. In contrast, endonuclease R . SinI did not exhibit such a similarity to other restriction enzymes.
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Affiliation(s)
- C Karreman
- Department of Medical Biochemistry, Sylvius Laboratories, University of Leiden, The Netherlands
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14
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Padhy RN, Hottat FG, Coene MM, Hoet PP. Restriction analysis and quantitative estimation of methylated bases of filamentous and unicellular cyanobacterial DNAs. J Bacteriol 1988; 170:1934-9. [PMID: 2832390 PMCID: PMC211053 DOI: 10.1128/jb.170.4.1934-1939.1988] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The DNAs of strains of three cyanobacterial genera (Anabaena, Plectonema, and Synechococcus) were found to be partially or fully resistant to many restriction endonucleases. This could be due to the absence of specific sequences or to modifications, rendering given sequences resistant to cleavage. The latter explanation is substantiated by the content of N6-methyladenine and 5-methylcytosine in these genomes, which is high in comparison with that in other bacterial genomes. dcm- and dam-like methylases are present in the three strains (based on the restriction patterns obtained with the appropriate isoschizomeric enzymes). Their contribution to the overall content of methyladenine and methylcytosine in the genomes was calculated. Partial methylation of GATC sequences was observed in Anabaena DNA. In addition, the GATC methylation patterns might not have been random in the three cyanobacterial DNA preparations, as revealed by the appearance of discrete fragments (possibly of plasmid origin) withstanding cleavage by DpnI (which requires the presence of methyladenine in the GATC sequence).
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Affiliation(s)
- R N Padhy
- Microbiology and Genetics Unit, University of Louvain Medical School, Brussels, Belgium
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15
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16
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17
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Gallagher ML, Burke WF. Sequence-specific endonuclease from the transformable cyanobacteriumAnacystis nidulansR2. FEMS Microbiol Lett 1985. [DOI: 10.1111/j.1574-6968.1985.tb01618.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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18
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Herrero A, Elhai J, Hohn B, Wolk CP. Infrequent cleavage of cloned Anabaena variabilis DNA by restriction endonucleases from A. variabilis. J Bacteriol 1984; 160:781-4. [PMID: 6094490 PMCID: PMC214805 DOI: 10.1128/jb.160.2.781-784.1984] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
A cosmid vector has been constructed, using a lambda replicon. A library of cosmids from Anabaena variabilis ATCC 29413 based on use of this vector is shown to be highly deficient in sites for the two type II restriction endonucleases found in that organism.
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