151
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Abstract
A 15,8-kilobase pair fragment of BALB/c mouse liver DNA, cloned in the Charon 4A lambda phage vector system, was shown to contain the mu heavy chain constant region (CHmu) gene for the mouse immunoglobulin M. In addition, this fragment of DNA contains at least two J genes, used to code for the carboxyl terminal portion of heavy chain variable regions. These genes are located in genomic DNA about eight kilobase pairs to the 5' side of the CHmu gene. The complete nucleotide sequence of a 1120-base pair stretch of DNA that includes the two J genes has been determined.
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152
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Schumm JW, Moore DD, Blattner FR, Howe MM. Correlation of the genetic and physical maps in the central region of the bacteriophage Mu genome. Virology 1980; 105:185-95. [PMID: 6251604 DOI: 10.1016/0042-6822(80)90166-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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153
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Abstract
A map of bacteriophage lambda was constructed, including accurate positions for all 41 cut sites made by 12 different restriction enzymes. Over 100 fragments from single, multiple, and partial enzyme digestions were measured versus standards that were calibrated with respect to DNA molecules of known sequence. The data were subjected to least-squares analysis to assign map coordinates. In no case did a fragment size predicted from the map differ from the measurement of the fragment by more than +/- 5%. This low error rate was consistent in all size ranges of fragments. The total length of lambda was calculated as 49,133 nucleotide pairs. This probably is accurate to within 500 base pairs.
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154
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de Wet JR, Daniels DL, Schroeder JL, Williams BG, Denniston-Thompson K, Moore DD, Blattner FR. Restriction maps for twenty-one Charon vector phages. J Virol 1980; 33:401-10. [PMID: 6245241 PMCID: PMC288556 DOI: 10.1128/jvi.33.1.401-410.1980] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The mapping of the sites of cleavage of nine restriction endonucleases (EcoRI, HindIII, BamHI, SalI, KpnI, SstI, BglII, XhoI, and XbaI) on 21 Charon phage vectors is described. Maps of individual subsections were obtained and then combined to assemble the complete vector maps. Calculations of maximum and minimum sizes of inserts which may be carried by the vectors using different restriction endonucleases or pairs of restriction endonucleases are presented. The regions mapped include several parts of phi 80 that had not been mapped previously.
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155
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Tucker PW, Marcu KB, Slightom JL, Blattner FR. Structure of the constant and 3' untranslated regions of the murine gamma 2b heavy chain messenger RNA. Science 1979; 206:1299-303. [PMID: 117548 DOI: 10.1126/science.117548] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The complete coding sequence for the constant region of the mouse gamma 2b immunoglobulin heavy chain and the 3' untranslated region has been determined. The coding portion of the sequence is 1008 nucleotides long (amino acid residues 114 to 449), and the 3' noncoding region contains 102 nucleotides preceeding the polyadenylate. An extra carboxyl-terminal lysine residue which had not been observed in the gamma 2b or other gamma subclass protein sequences occurs in the nucleotide sequence and is probably processed posttranslationally. A 17-nucleotide sequence occurs with slight variation twice in CH1 and once in CH2 domains in the same relative location but with different translational phase. This sequence may be the site of crossover in a gamma 2b . gamma 2a heavy chain variant, an indication of possible recombinational activity of some kind.
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156
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Tucker PW, Marcu KB, Newell N, Richards J, Blattner FR. Sequence of the cloned gene for the constant region of murine gamma 2b immunoglobulin heavy chain. Science 1979; 206:1303-6. [PMID: 117549 DOI: 10.1126/science.117549] [Citation(s) in RCA: 109] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The complete nucleotide sequence of the gamma 2b constant region gene cloned from BALB/c liver DNA is reported. The sequence of approximately 1870 base pairs includes the 5' flanking, 3' untranslated, and 3' flanking regions and three introns. The C gamma 2b coding region is divided by these introns into four segments corresponding to the homology domains and hinge region of the protein. The introns separating the hinge from the CH2 domain and the CH2 from the CH3 domain are small (106 and 119 base pairs). A larger intervening sequence of 314 base pairs separates the CH1 and hinge regions. The stretch of DNA comprising this large intron plus the hinge shows a strong homology with the other CH domains.
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157
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Gross CA, Blattner FR, Taylor WE, Lowe PA, Burgess RR. Isolation and characterization of transducing phage coding for sigma subunit of Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A 1979; 76:5789-93. [PMID: 392509 PMCID: PMC411736 DOI: 10.1073/pnas.76.11.5789] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A transducing phage has been isolated with codes for the sigma subunit of Escherichia coli RNA polymerase. Transducing phage were selected from E. coli shotgun collections of HindIII or Sac I fragments cloned into Charon 25, a new bacteriophage lambda vector that is capble of forming lyosogens at high temperature. Transduction of an E. coli strain carrying a temperature-sensitive mutation in the sigma gene was used for the selection. The positions of restriction sites for Sac I, HindIII, Xho I, Bgl II, and Kpn I in the cloned bacterial DNA segments were determined. Phage containing the HindIII fragment complement both primase (dnaG) and sigma (rpoD) whereas those containing the Sac I fragment complement only sigma. Results of analyses of the proteins made both in vivo after infection of UV-irradiated cells and in vitro in a coupled transcription/translation system suggest that a Sac I site separates the promoter for sigma from the sigma structural gene. The direction of transcription of sigma was determined to be clockwise with respect to the E. coli genetic map.
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158
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Williams BG, Blattner FR. Construction and characterization of the hybrid bacteriophage lambda Charon vectors for DNA cloning. J Virol 1979; 29:555-75. [PMID: 372561 PMCID: PMC353190 DOI: 10.1128/jvi.29.2.555-575.1979] [Citation(s) in RCA: 117] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Twenty hybrid lambda phages especially designed for molecular cloning have been constructed and named Charon phages. These phages differ in the ranges of sizes of DNA fragments that may be inserted, by the selections and screens which may be used to isolate and detect the incorporation of cloned fragments, by the way transcription of the cloned fragment may be controlled, by the different restriction enzymes that can be used for cloning, by the phage immunities that may be employed for controlling replication and transcription, and by the biological safety features that they contain. The crosses used to produce the vectors are described, and their genealogy is discussed. The structure of each vector has been verified by genetic tests, by DNA length determinations, by electron micrographic analysis of DNA heteroduplexes, and by gel electrophoresis of restriction enzyme digests. In the course of these constructions, a new EcoRI site was found in a derivative of lambda Aam32Bam1 which maps very near the left cohesive end of lambda.
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159
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Moore DD, Denniston-Thompson K, Kruger KE, Furth ME, Williams BG, Daniels DL, Blattner FR. Dissection and comparative anatomy of the origins of replication of lambdoid phages. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 1979; 43 Pt 1:155-63. [PMID: 157834 DOI: 10.1101/sqb.1979.043.01.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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160
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Smithies O, Blechl AE, Denniston-Thompson K, Newell N, Richards JE, Slightom JL, Tucker PW, Blattner FR. Cloning human fetal gamma globin and mouse alpha-type globin DNA: characterization and partial sequencing. Science 1978; 202:1284-9. [PMID: 725604 DOI: 10.1126/science.725604] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Two globin-related clones isolated from collections of bacteriophages containing unfractionated Eco RI fragments of human and mouse DNA were characterized. Charon3AHs51.1Hbgamma includes 2.7 kilobase pairs of human DNA containing a large part of a fetal gamma globin chain structural gene; Charon 3AMm30.5 includes 4.7 kilobase pairs of mouse DNA related to alpha globin. The human fetal gamma globin gene has within its coding region two intervening sequences of noncoding DNA, IVS 1 and IVS 2, of approximately 1-0 and 900 base pairs. Sequence IVS 1 is located at the position of one of the two intervening sequences occurring in adult globin genes; IVS 2 is located at the position of the other.
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161
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Blattner FR, Blechl AE, Denniston-Thompson K, Faber HE, Richards JE, Slightom JL, Tucker PW, Smithies O. Cloning human fetal gamma globin and mouse alpha-type globin DNA: preparation and screening of shotgun collections. Science 1978; 202:1279-84. [PMID: 725603 DOI: 10.1126/science.725603] [Citation(s) in RCA: 316] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Shotgun collections of Charon 3A bacteriophages containing Eco RI fragments of human and mouse DNA were constructed with the use of in vitro packaging. Plaques were screened by hybridization, and globin-specific clones were isolated from both human (Charon 3AHs51.1) and mouse (Charon 3AMm30.5). The fragments cloned were detected in unfractionated genomic DNA by the Southern method of hybridization.
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162
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Abstract
A least-squares procedure has been developed to aid in deriving restriction-fragment maps once the order of cutsites has been determined. A computer program which carries out this method can be used to map either linear or circular molecules.
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163
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Furth ME, Blattner FR, McLeester C, Dove WF. Genetic structure of the replication origin of bacteriophage lambda. Science 1977; 198:1046-51. [PMID: 929186 DOI: 10.1126/science.929186] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A fragment of bacteriophage lambda DNA produced by the restriction endonuclease Eco RI and extending from the immunity region to a point inside gene O is found to have a fully functional origin of replication. Seven ori- mutations of lambda cluster in a small region just to the left of the Eco RI cleavage site which defines the right end of this fragment. These mutations lie within gene O.
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164
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Denniston-Thompson K, Moore DD, Kruger KE, Furth ME, Blattner FR. Physical structure of the replication origin of bacteriophage lambda. Science 1977; 198:1051-6. [PMID: 929187 DOI: 10.1126/science.929187] [Citation(s) in RCA: 96] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The nucleotide sequence of part of the replication region of wild-type bacteriophage lambda and of four mutants defective in the origin of DNA replication (ori-) has been determined. Three of the ori- mutations are small deletions, and one is a transversion. The sequence of the origin region, defined by these mutations, contains a number of unusual features.
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165
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Moore DD, Denniston-Thompson K, Furth ME, Williams BG, Blattner FR. Construction of chimeric phages and plasmids containing the origin of replication of bacteriophage lambda. Science 1977; 198:1041-6. [PMID: 929185 DOI: 10.1126/science.929185] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Segments of the replication control region of bacteriophage lambda (lambda) and lambda mutants defective in replication were attached in vitro to the phi80 phage vector Charon 3 and to the plasmid vector mini Col El (pVH51). The chimeric phages and plasmids have been used to localize the origin of lambda DNA replication and to facilitate a structural analysis of the lambda replicator.
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166
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Williams BG, Blattner FR, Jaskunas SR, Nomura M. Insertion of DNA carrying ribosomal protein genes of Escherichia coli into Charon vector phages. J Biol Chem 1977; 252:7344-54. [PMID: 332692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
DNA fragments from lambdaspc1 and lambdafus2, carrying ribosomal protein genes from Escherichia coli, were inserted into lambda phage vectors Charon 3 and Charon 4. Eight of the resulting clones were characterized by agarose gel electrophoresis of EcoRI digests, analytical CsCl equilibrium centrifugation, and electron micrographic analysis of heteroduplexes. In each case, the identity, order, and orientation of each cloned fragment was determined. In all, 8 of the 12 EcoRI fragments of lambdafus2 were cloned in various arrangements. In the accompanying paper, genes for 15 ribosomal and related proteins and three bacterial promoters were detected in these phages. In addition, four of the hybrid phages carried fragments of lambda-DNA including the phage origin of replication (ori), the late promoter, PR', and the cohesive ends (cos site) in both orientations. The latter phages yield a circularly permuted collection of DNA molecules.
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167
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Jaskunas SR, Fallon AM, Nomura M, Williams BG, Blattner FR. Expression of ribosomal protein genes cloned in Charon vector phages and identification of their promoters. J Biol Chem 1977; 252:7355-64. [PMID: 332693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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168
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Williams BG, Blattner FR, Jaskunas SR, Nomura M. Insertion of DNA carrying ribosomal protein genes of Escherichia coli into Charon vector phages. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(19)66973-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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169
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Blattner FR, Williams BG, Blechl AE, Denniston-Thompson K, Faber HE, Furlong L, Grunwald DJ, Kiefer DO, Moore DD, Schumm JW, Sheldon EL, Smithies O. Charon phages: safer derivatives of bacteriophage lambda for DNA cloning. Science 1977; 196:161-9. [PMID: 847462 DOI: 10.1126/science.847462] [Citation(s) in RCA: 745] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The Charon lambda bacteriophages have been developed as vectors for cloning. Their construction incorporates mutations that make them simple to use and also greatly increases their safety for the biological containment of cloned recombinant DNA. Three of the Charon vector phages, 3A, 4A, and 16A, have been certified for use as EK2 vector-host systems, when propagated in bulk in a special bacterial host, DP50SupF. We present here some of the data on which the safety of these systems was evaluated. DNA fragments ranging in size from 0 to 2.2 X 10(4) base pairs can be cloned in these EK2 Charon phages.
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170
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Fiandt M, Szybalski W, Blattner FR, Jaskunas SR, Lindahl L, Nomura M. Organization of ribosomal protein genes in Escherichia coli. I. Physical structure of DNA from transducing lambda phages carrying genes from the aroE-str region. J Mol Biol 1976; 106:817-35. [PMID: 789899 DOI: 10.1016/0022-2836(76)90267-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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171
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Smith DI, Blattner FR, Davies J. The isolation and partial characterization of a new restriction endonuclease from Providencia stuartii. Nucleic Acids Res 1976; 3:343-53. [PMID: 768923 PMCID: PMC342905 DOI: 10.1093/nar/3.2.343] [Citation(s) in RCA: 146] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We describe the isolation of a new class 2 restriction endonuclease from Providencia stuartii 164. Using the procedure of osmotic shock treatment, we have partially purified this enzyme (Pst 1) and have begun preliminary work to characterize its specificity and requirements. Pst 1 requires Mg++ as the only cofactor and produces more than 18 cleavages in wild type lambda. We have determined the location of 7 of these cleavages by the use of deletion and insertion mutants of lambda.
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172
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Shinnick TM, Lund E, Smithies O, Blattner FR. Hybridization of labeled RNA to DNA in agarose gels. Nucleic Acids Res 1975; 2:1911-29. [PMID: 1103090 PMCID: PMC343556 DOI: 10.1093/nar/2.10.1911] [Citation(s) in RCA: 132] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Specific DNA restriction endonuclease fragments can be identified after electrophoresis in agarose gels by hybridization in the gel (in situ) to radioactive homologous RNA. RNA-DNA hybrids are detected by autoradiography of the gel. Comparison of band patterns of the autoradiogram and the ethidium bromide stained gel allows the identification of the DNA fragment which is complementary to the RNA probe. The technique is rapid, easy and inexpensive. It is sensitive enough to detect individual genes in a mixture of fragments produced by restriction enzyme digestion of complex cellular DNA. We have used this technique to determine which of the Hin III and Eco R1 fragments of phi80d3ilv+su+7 and E. coli DNAs contain the 5S, 16S and 23S ribosomal RNA (rRNA) genes of E. coli.
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173
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Dahlberg JE, Blattner FR. Sequence of the promoter-operator proximal region of the major leftward RNA of bacteriophage lambda. Nucleic Acids Res 1975; 2:1441-58. [PMID: 1178525 PMCID: PMC343515 DOI: 10.1093/nar/2.9.1441] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The sequence of the first 149 nucleotides of the major leftward RNA of bacteriophage lambda has been determined. Preliminary sequence information was also obtained for a portion of the untranscribed area immediately upstream of the point on the template when RNA synthesis normally starts. Several restriction endonuclease sites, deletion endpoints, and single base changes have been localized within the sequence. The first potential translation initiation codon which is not followed by an in-phase termination codon is a GUG located 90 nucleotides from the transcription startpoint.
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174
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Blattner FR, Fiandt M, Hass KK, Twose PA, Szybalski W. Deletions and insertions in the immunity region of coliphage lambda: revised measurement of the promoter-startpoint distance. Virology 1974; 62:458-71. [PMID: 4432374 DOI: 10.1016/0042-6822(74)90407-3] [Citation(s) in RCA: 111] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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175
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Skinner DM, Beattie WG, Blattner FR, Stark BP, Dahlberg JE. The repeat sequence of a hermit crab satellite deoxyribonucleic acid is (-T-A-G-G-)n-(-A-T-C-C-)n. Biochemistry 1974; 13:3930-7. [PMID: 4607234 DOI: 10.1021/bi00716a018] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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176
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Blattner FR, Dahlberg JE, Boettiger JK, Fiandt M, Szybalski W. Distance from a promoter mutation to an RNA synthesis startpoint on bacteriophage lambda DNA. NATURE: NEW BIOLOGY 1972; 237:232-6. [PMID: 4504486 DOI: 10.1038/newbio237232a0] [Citation(s) in RCA: 47] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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177
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Blattner FR, Dahlberg JE. RNA synthesis startpoints in bacteriophage lambda: are the promoter and operator transcribed? NATURE: NEW BIOLOGY 1972; 237:227-32. [PMID: 4556643 DOI: 10.1038/newbio237227a0] [Citation(s) in RCA: 103] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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