51
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Studies of low molecular weight RNA from cells infected with adenovirus 2. I. The sequences at the 3' end of VA-RNA I. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)38341-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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52
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Bertrand K, Korn LJ, Lee F, Yanofsky C. The attenuator of the tryptophan operon of Escherichia coli. Heterogeneous 3'-OH termini in vivo and deletion mapping of functions. J Mol Biol 1977; 117:227-47. [PMID: 340702 DOI: 10.1016/0022-2836(77)90032-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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53
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Kozak M, Shatkin AJ. Sequences and properties of two ribosome binding sites from the small size class of reovirus messenger RNA. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)39934-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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54
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55
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56
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57
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Abstract
The start sites of the araC and araBAD gene messenger of E. coli were located by transcription in vitro from short DNA fragments, by high magnification electron microscopy and by genetic mapping. Transcription for these messengers proceeds in opposite directions from the start sites that are 150 base pairs apart. Transcription from the araBAD promoter requires araC protein plus arabinose and CAP protein plus cyclic AMP. In the experiments performed in vitro, inducing the araBAD promoter represses activity of the araC promoter.
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58
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Sklar J, Weissman S, Musso RE, DiLauro R, de Crombrugghe B. Determination of the nucleotide sequence of part of the regulatory region for the galactose operon from Escherichia coli. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)40424-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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59
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Sugimoto K, Sugisaki H, Okamoto T, Takanami M. Studies on bacteriophage fd DNA. IV. The sequence of messenger RNA for the major coat protein gene. J Mol Biol 1977; 111:487-507. [PMID: 864706 DOI: 10.1016/s0022-2836(77)80065-x] [Citation(s) in RCA: 117] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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60
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Subramanian KN, Dhar R, Weissman SM. Nucleotide sequence of a fragment of SV40 DNA that contains the origin of DNA replication and specifies the 5' ends of "early" and "late" viral RNA. I. Mapping of the restriction endonuclease sites within the EcoRII-G fragment and strategy employed for its sequence analysis. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)32835-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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61
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Subramanian KN, Dhar R, Weissman SM. Nucleotide sequence of a fragment of SV40 DNA that contains the origin of DNA replication and specifies the 5' ends of "early" and "late" viral RNA. III. Construction of the total sequence of EcoRII-G fragment of SV40 DNA. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)32837-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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62
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Subramanian KN, Dhar R, Weissman SM, Ghosh PK. Nucleotide sequence of a fragment of SV40 DNA that contains the origin of DNA replication and specifies the 5' ends of "early" and "late" viral RNA. II. Sequences of T1 and pancreatic ribonuclease digestion products of RNA transcripts prepared from subfragments of EcoRII-G. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)32836-3] [Citation(s) in RCA: 6] [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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63
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Subramanian KN, Ghosh PK, Dhar R, Thimmappaya B, Zain SB, Pan J, Weissman SM. The primary structure of regions of SV 40 DNA encoding the ends of mRNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1977; 19:157-64. [PMID: 190641 DOI: 10.1016/s0079-6603(08)60916-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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64
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Dhar R, Subramanian KN, Pan J, Weissman SM. Nucleotide sequence of a fragment of SV40 DNA that contains the origin of DNA replication and specifies the 5' ends of "early" and "late" viral RNA. IV. Localization of the SV40 DNA complementary to the 5' ends of viral mRNA. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)32838-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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65
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66
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Axelrod N. Transcription of bacteriophage phi-X174 in vitro: selective initiation with oligonucleotides. J Mol Biol 1976; 108:753-70. [PMID: 1018323 DOI: 10.1016/s0022-2836(76)80115-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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67
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Bothwell AL, Garber RL, Altman S. Nucleotide sequence and in vitro processing of a precursor molecule to Escherichia coli 4.5 S RNA. J Biol Chem 1976. [DOI: 10.1016/s0021-9258(17)32909-5] [Citation(s) in RCA: 86] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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68
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Hewish DR, Smith KK, Spencer JH. Nucleotide clusters in deoxyribonucleic acids. XIV. Pyrimidine oligonucleotides of the left and right halves and lambdadv region of bacteriophage lambda DNA. Virology 1976; 74:363-76. [PMID: 982832 DOI: 10.1016/0042-6822(76)90342-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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69
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Segal S, Garner M, Singer MF, Rosenberg M. In situ hybridization of repetitive monkey genome sequences isolated from defective simian virus 40 DNA. Cell 1976; 9:247-57. [PMID: 184962 DOI: 10.1016/0092-8674(76)90116-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The origin of a repetitive monkey DNA sequence that is incorporated into a defective simian virus 40 genome has been studied. A fragment (about 140 base pairs in length) containing essentially all the repetitive monkey DNA present in the defective and few, if any, SV40 sequences can be cleaved from the purified defective DNA by restriction endonucleases Hind(II and III). Radioactive cRNA prepared with the isolated fragment as template was hybridized in situ to African green monkey chromosomes. The results indicate that all or part of the sequence in question occurs at both centromeric and noncentromeric positions in many, but not all, chromosomes. Of the typical 60 chromosomes, between nine and eleven hybridize with the cRNA in noncentromeric regions.
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70
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Elton RA, Russell GJ, Subak-Sharpe JH. Doublet frequencies and codon weighting in the DNA of Escherichia coli and its phages. J Mol Evol 1976; 8:117-35. [PMID: 787545 DOI: 10.1007/bf01739098] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A compilation of nucleic acid sequences from E. coli and its phages has been analysed for the frequency of occurrence of nearest neighbour base doublets and codons. Several statistically significant deviations from random are found in both doublet and codon frequencies. The deviations in E. coli also appear to occur in lambda and in the coat protein gene of MS2, whereas T4 and other parts of the MS2 genome show different sequence properties. These and other findings are discussed in relation to the hypothesis that rapidity of translation of mRNAs in the E. coli system is dependent on doublet frequency and codon usage patterns.
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71
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72
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Smith LH, Sinsheimer RL. The in vitro transcription units of bacteriophage phiX174. III. Initiation with specific 5' end oligonucleotides of in vitro phiX174 RNA. J Mol Biol 1976; 103:711-35. [PMID: 781284 DOI: 10.1016/0022-2836(76)90205-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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73
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Sogin ML, Pace NR. Nucleotide sequence of 5 S ribosomal RNA precursor from Bacillus subtilis. J Biol Chem 1976. [DOI: 10.1016/s0021-9258(17)33463-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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74
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Squires C, Lee F, Bertrand K, Squires CL, Bronson MJ, Yanofsky C. Nucleotide sequence of the 5' end of tryptophan messenger RNA of Escherichia coli. J Mol Biol 1976; 103:351-81. [PMID: 781271 DOI: 10.1016/0022-2836(76)90317-x] [Citation(s) in RCA: 100] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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75
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Lee F, Squires CL, Squires C, Yanofsky C. Termination of transcription in vitro in the Escherichia coli tryptophan operon leader region. J Mol Biol 1976; 103:383-93. [PMID: 781272 DOI: 10.1016/0022-2836(76)90318-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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76
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ATPase activity required for termination of transcription by the Escherichia coli protein factor rho. J Biol Chem 1976. [DOI: 10.1016/s0021-9258(17)33618-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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77
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Brown RD, Brown DD. The nucleotide sequence adjoining the 3' end of the genes coding for oocyte-type 5 S ribosomal RNA in Xenopus. J Mol Biol 1976; 102:1-14. [PMID: 944788 DOI: 10.1016/0022-2836(76)90070-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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78
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Mitchell DH, Reznikoff WS, Beckwith J. Genetic fusions that help define a transcription termination region in Escherichia coli. J Mol Biol 1976; 101:441-57. [PMID: 772220 DOI: 10.1016/0022-2836(76)90239-4] [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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79
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Weissman SM, Subramanian KN, Dhar R, Zain B, Pan J. SV40 DNA sequences as an example of the structure of genes functioning in animal cell nuclei. MEDICAL AND PEDIATRIC ONCOLOGY 1976; 2:259-63. [PMID: 185508 DOI: 10.1002/mpo.2950020306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent studies of the structure of messenger RNA have demonstrated the existence of untranslated sequences of the 3' and 5' end of the messages. In addition analysis of transcription in vitro has indicated that the nucleotide sequence U6 purine may be part of a transcription termination signal in prokaryotes. Recently it has been possible to determine the sequence of extensive portions of the DNA of SV40 virus. This article reviews the analogies between certain of these sequences and sequences available from prokaryotic messengers and DNAs. Unusual structures, including blocks of AT-rich and GC-rich segment sections and symmetric regions in the DNA near the origin of DNA replication, have been demonstrated and the distribution of stretches of 6 or more deoxyadenylic acids in the DNA of SV40 is consistent with some rho for these sequences in animal cells, either as terminators of transcription or as sites where degradation of transcripts is initiated or sites related to the selective rejection or degradation of transcipts.
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80
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Kwong TC, Steege D, Lawler D, Söll D. Bacteriophage lambda induction causes increased production of E. coli lysine transfer RNA. Arch Biochem Biophys 1975; 170:651-8. [PMID: 1103738 DOI: 10.1016/0003-9861(75)90161-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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81
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Darlix JL, Horaist M. Existence and possible roles of transcriptional barriers in T7 DNA early region as shown by electron microscopy. Nature 1975; 256:288-92. [PMID: 1143328 DOI: 10.1038/256288a0] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Transcription of T7 DNA in vitro by Escherichia coli RNA polymerase in the absence or presence of termination factor rho has been studied extensively using electron microscopy. It is demonstrated that sequences located between the early genes behave as transient transcriptional barriers in the absence of rho and are recognised both as rho-dependent terminators and as RNaseIII cleavage sites.
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82
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Bertrand K, Korn L, Lee F, Platt T, Squires CL, Squires C, Yanofsky C. New features of the regulation of the tryptophan operon. Science 1975; 189:22-6. [PMID: 1094538 DOI: 10.1126/science.1094538] [Citation(s) in RCA: 205] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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83
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84
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Brockman WW, Gutai MW, Nathans D. Evolutionary variants of simian virus 40: characterization of cloned complementing variants. Virology 1975; 66:36-52. [PMID: 166504 DOI: 10.1016/0042-6822(75)90177-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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85
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86
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Rosenberg M, Weissman S, deCrombrugghe B. Termination of transcription in bacteriophage lambda. Heterogeneous, 3'-terminal oligo-adenylate additions and the effects of rho factor. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41367-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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87
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Lebowitz P, Bloodgood R. Transcription of simian virus 40 DNA by Escherichia coli RNA polymerase: synthesis of a DNA-RNA hybrid and discrete RNAs under restrictive transcription conditions. J Mol Biol 1975; 94:183-201. [PMID: 167179 DOI: 10.1016/0022-2836(75)90077-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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88
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Ro-Choi TS, Choi YC, Henning D, McCloskey J, Busch H. Nucleotide sequence of U-2 ribonucleic acid. The sequence of the 5'-terminal oligonucleotide. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41486-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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89
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90
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Abstract
A doublet frequency count (set of frequencies of the 16 possible two-base sequences) can be calculated from the experimentally determined overall sequence of a nucleic acid. In this paper, a statistical methodology is developed for comparing such counts with random, with others of the same type or with doublet proportions found in whole DNAs. The methods are applied to two major categories of sequenced RNAs. It is found that vertebrate ribosomal and transfer RNAs show significant differences from the overall vertebrate DNA pattern, especially in the frequency of the doublet CG. Bacterial rRNA and tRNA, on the other hand, show less dissimilarity from total DNA. In the RNA of the small bacteriophage MS2, the doublet frequencies of the translated regions of the genome resemble those in the host E. coli, whereas those in the intercistronic regions differ substantially. All these findings are discussed in relation to the origin, evolution and selection of the nucleic acids concerned.
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91
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Kaplan DA, Nierlich DP. Initiation and transcription of a set of transfer ribonucleic acid genes in vitro. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41874-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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92
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Abstract
The nucleotide sequence of the lac promoter-operator region has been determined. The 122 base pairs comprising this region include the recognition sites for RNA polymerase, the positive regulatory protein, CAP, and the negative regulatory protein, the repressor. Identification of mutant variants of the sequence combined with the in vitro biochemical studies of others has allowed us to tentatively identify the recognition site for each of these proteins, and to suggest how CAP might act at a distance to affect the interaction of RNA polymerase with the promoter.
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93
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94
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Sanger F, Donelson JE, Coulson AR, Kössel H, Fischer D. Determination of a nucleotide sequence in bacteriophage f1 DNA by primed synthesis with DNA polymerase. J Mol Biol 1974; 90:315-33. [PMID: 4616099 DOI: 10.1016/0022-2836(74)90376-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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95
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Forget BG, Marotta CA, Weissman SM, Verma IM, McCaffrey RP, Baltimore D. Nucleotide sequences of human globin messenger RNA. Ann N Y Acad Sci 1974; 241:290-309. [PMID: 4611306 DOI: 10.1111/j.1749-6632.1974.tb21888.x] [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: 01/11/2023]
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96
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Peters GG, Hayward RS. Transcriptional termination in vitro: the 3'-terminal sequence of coliphage T7 "early" RNA. Biochem Biophys Res Commun 1974; 61:809-16. [PMID: 4616695 DOI: 10.1016/0006-291x(74)91029-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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97
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Rosenberg M, Kramer RA, Steitz JA. T7 early messenger RNAs are the direct products of ribonuclease III cleavage. J Mol Biol 1974; 89:777-82. [PMID: 4615167 DOI: 10.1016/0022-2836(74)90052-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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98
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Kramer RA, Rosenberg M, Steitz JA. Nucleotide sequences of the 5' and 3' termini of bacteriophage T7 early messenger RNAs synthesized in vivo: evidence for sequence specificity in RNA processing. J Mol Biol 1974; 89:767-76. [PMID: 4449132 DOI: 10.1016/0022-2836(74)90051-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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99
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Bronson MJ, Yanofsky C. Letter to the editor: Characterization of mutations in the tryptophan operon of Escherichia coli by RNA nucleotide sequencing. J Mol Biol 1974; 88:913-5. [PMID: 4610162 DOI: 10.1016/0022-2836(74)90407-0] [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: 01/11/2023]
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100
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Peters GG, Hayward RS. Dinucleotide sequences in the regions of T7 DNA coding for termination of early transcription. EUROPEAN JOURNAL OF BIOCHEMISTRY 1974; 48:199-208. [PMID: 4614973 DOI: 10.1111/j.1432-1033.1974.tb03757.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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