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Abstract
Enterohemorrhagic E. coli is a significant human pathogen that can cause severe disease due to the release of Shiga toxins. The toxins are encoded within lysogenic bacteriophage and controlled by antitermination of the phage late promoter, PR′. This promoter is always active, but terminated immediately downstream during lysogeny. A byproduct of antitermination regulation is transcription of a short RNA that is thought to be nonfunctional. Here we demonstrate that in Shiga toxin-encoding phages, this short RNA is a Hfq-binding regulatory small RNA. The small RNA represses toxin production threefold under lysogenic conditions and promotes high cell density growth. Lysogenic bacteriophages are highly abundant and our results suggest that antiterminated phage promoters may be a rich source of regulatory RNAs. Enterohemorrhagic Escherichia coli is a significant human pathogen that causes disease ranging from hemorrhagic colitis to hemolytic uremic syndrome. The latter can lead to potentially fatal renal failure and is caused by the release of Shiga toxins that are encoded within lambdoid bacteriophages. The toxins are encoded within the late transcript of the phage and are regulated by antitermination of the PR′ late promoter during lytic induction of the phage. During lysogeny, the late transcript is prematurely terminated at tR′ immediately downstream of PR′, generating a short RNA that is a byproduct of antitermination regulation. We demonstrate that this short transcript binds the small RNA chaperone Hfq, and is processed into a stable 74-nt regulatory small RNA that we have termed StxS. StxS represses expression of Shiga toxin 1 under lysogenic conditions through direct interactions with the stx1AB transcript. StxS acts in trans to activate expression of the general stress response sigma factor, RpoS, through direct interactions with an activating seed sequence within the 5′ UTR. Activation of RpoS promotes high cell density growth under nutrient-limiting conditions. Many phages utilize antitermination to regulate the lytic/lysogenic switch and our results demonstrate that short RNAs generated as a byproduct of this regulation can acquire regulatory small RNA functions that modulate host fitness.
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Atkinson BL, Gottesman ME. The Escherichia coli rpoB60 mutation blocks antitermination by coliphage HK022 Q-function. J Mol Biol 1992; 227:29-37. [PMID: 1522593 DOI: 10.1016/0022-2836(92)90679-e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The lambdoid bacteriophage regulate gene expression by suppressing transcription terminators. Although similar in sequence to lambda, HK022 lacks an analogue to the lambda N antitermination gene and a distinct nutR sequence. To define the HK022 antitermination system, we plated the phage on Escherichia coli nus mutants that inhibit lambda N function. Only rpoB60 (also called nusC60) blocked HK022 lytic growth. Analyses of HK022-lambda hybrid phage suggested that a HK022 function analogous to lambda Q was inhibited by rpoB60. This result was confirmed with pR'-tR'-galK fusions. HK022 Q-protein suppressed tR' in wild-type but not in rpoB60 mutants. The lambda Q-protein, although inhibited by rpoB60, was more active than the HK022 analogue. A single amino acid difference between the two Q-proteins accounts for the phenotype. Changing the penultimate residue of HK022 Q from alanine to the lambda threonine generated a phage that could propagate on rpoB60 hosts. Host and phage mutations that permitted HK022 growth in rpoB60 strains were characterized. The bacterial suppressors were located in the Escherichia coli nusB gene. The phage suppressors represented recessive mutations in a HK022 b-region sequence encoding an open reading frame of 73 codons.
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Affiliation(s)
- B L Atkinson
- Institute of Cancer Research, Columbia University, College of Physicians and Surgeons, New York, NY 10032
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3
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Barik S, Ghosh B, Whalen W, Lazinski D, Das A. An antitermination protein engages the elongating transcription apparatus at a promoter-proximal recognition site. Cell 1987; 50:885-99. [PMID: 3040263 DOI: 10.1016/0092-8674(87)90515-0] [Citation(s) in RCA: 117] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
As a transcriptional activator, the N protein of phage lambda acts to suppress transcription termination by recognizing a promoter-proximal site, nut, which is separated from the terminators by thousands of base pairs. We demonstrate here that N interacts with the elongating RNA polymerase in transit through the boxB domain of nut. This interaction leads to the stable association of N as an integral component of the transcription apparatus. During subsequent elongation, N translocates along with polymerase through several defined terminators positioned beyond nut. Therefore, by being an operon-specific subunit of the transcription apparatus, N presumably prevents the interaction of polymerase with termination signals.
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4
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Brendel V, Hamm GH, Trifonov EN. Terminators of transcription with RNA polymerase from Escherichia coli: what they look like and how to find them. J Biomol Struct Dyn 1986; 3:705-23. [PMID: 3078109 DOI: 10.1080/07391102.1986.10508457] [Citation(s) in RCA: 99] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We present here a compilation of prokaryotic transcription terminator sequences (ref. 1-152). The compilation includes 49 independent terminators, 52 speculated independent terminators, 27 sites shown to function in vivo, and some 20 proven or speculated rho-dependent terminators. In addition to the well-known features of independent terminators (dyad symmetry and T-run), two consensus are found: CGGG(C/G) upstream and TCTG downstream of the termination point. A subset of the collection of sequence has been used to construct a computer algorithm to locate independent terminators by sequence analysis.
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Affiliation(s)
- V Brendel
- Department of Polymer Research, Weizmann Institute of Science, Rehovot, Israel
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5
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Wiggins BA, Hilliker S. Genetic and DNA mapping of the late regulation and lysis genes of Salmonella bacteriophage P22 and coliphage lambda. J Virol 1985; 56:1030-3. [PMID: 2933531 PMCID: PMC252680 DOI: 10.1128/jvi.56.3.1030-1033.1985] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Genetic and DNA heteroduplex analyses of lambda imm22 hybrid phages were used to compare the Salmonella bacteriophage P22 and coliphage lambda genes which control late gene regulation and lysis. Homologous DNA sequences were correlated with P22 gene 23 and lambda gene Q (late gene regulation) and with P22 gene 13 and lambda gene S (lysis control). Nonhomologous DNA sequences were correlated with P22 gene 19 and lambda gene R (lysozyme and endolysin) and with the region encoding the P22 alpha and lambda 6S transcripts.
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6
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Abstract
The Escherichia coli sulA gene product is a highly unstable protein, whose synthesis in response to DNA damage is associated with an inhibition of septation. Genetic evidence as well as sequence information suggests that the sulA gene is part of the E. coli SOS system and is induced after DNA damage. We have constructed a plasmid carrying only the sulA gene; this plasmid is stable only when it contains an amber mutation in the sulA structural gene. Using fragments of this plasmid, we have carried out in vitro transcription experiments and demonstrated one major start site for RNA transcription. We have mapped this initiation point to an adenylate residue 30 nucleotides before the protein start. Purified LexA protein completely abolishes this transcription, in agreement with the prediction made from the genetic and sequence information previously available.
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Luk KC, Szybalski W. Tandem transcription-termination sites in the late rightward operon of bacteriophage lambda. MOLECULAR & GENERAL GENETICS : MGG 1983; 189:289-97. [PMID: 6222243 DOI: 10.1007/bf00337819] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A transcription termination site (designated as t'R2) is located between the rightward late t'R1 terminator and the S gene of phage lambda. This t'R2 terminator is rightward and absolutely dependent on the rho factor, being about 45% effective in rho+ E. coli and only 6% in rho- cells at 30 degrees C. This 7.5-fold rho dependence of t'R2 is in contrast to that of tR1 (4.5 fold, from about 81% to 18%) and the partial rho dependence of t'R1 (1.4 fold, from 96% to 67%). At the elevated temperature of 42 degrees C, t'R2 becomes 1.5 times more leaky (with about 2.5-fold reduction in termination efficiency) than tR1 or t'R1 (with only 1.1-fold reduction) in rho+ hosts. The calculated joint efficiencies of t'R1 and t'R2 are 98% in rho+ cells at 30 degrees C. t'R2 is also active in vitro, but only in the presence of rho factor, whereas t'R1 is active both in the presence and absence of rho. However, the in vitro termination at t'R1 is enhanced about 1.7-fold by the rho factor. The properly oriented lambda nutR site together with the N gene function bring about almost complete antitermination at t'R2 (96% effective), but incomplete at t'R1 (72%). The termination points at t'R2 are located around 532-534 bp to the right of the s'R startpoint of the p'R-initiated RNA on lambda DNA (or 338-340 bp downstream of t'R1) and 66-68 bp to the left of the S gene, as determined by S1 mapping. The t'R2 termination points are located within a dyad symmetry region which, in the transcript, is able to form a hairpin structure consisting of 16 bp in the stem and 6 bases in the loop. It is proposed that t'R2 acts as a second terminator to block any readthrough transcription initiated at the late promoter p'R into the late genes of phage lambda.
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9
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Edlind TD, Ihler GM. Electron microscopic mapping of complementary sequences on single strands of bacteriophage lambda DNA. J Mol Biol 1982; 160:23-39. [PMID: 6294302 DOI: 10.1016/0022-2836(82)90129-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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10
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Kozak M. Analysis of ribosome binding sites from the s1 message of reovirus. Initiation at the first and second AUG codons. J Mol Biol 1982; 156:807-20. [PMID: 7120395 DOI: 10.1016/0022-2836(82)90143-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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11
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Daniels DL, Blattner FR. Nucleotide sequence of the Q gene and the Q to S intergenic region of bacteriophage lambda. Virology 1982; 117:81-92. [PMID: 6461127 DOI: 10.1016/0042-6822(82)90509-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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12
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Greenblatt J, McLimont M, Hanly S. Termination of transcription by nusA gene protein of Escherichia coli. Nature 1981; 292:215-20. [PMID: 6265785 DOI: 10.1038/292215a0] [Citation(s) in RCA: 113] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The nusA gene protein of Escherichia coli and N gene protein of bacteriophage lambda interact in vitro and cooperate in vivo to prevent transcription termination. In vitro the nusA gene protein causes RNA polymerase to pause in the tR2 terminator region of lambda DNA. A completed termination event at tR2 requires both the nusA gene protein and the previously described E. coli termination factor rho. The nusA gene protein is therefore both a transcription termination factor and a protein which couples antitermination factors to the elongating transcription complex.
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13
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Honigman A. Cloning and characterization of a transcription termination signal in bacteriophage lambda unresponsive to the N gene product. Gene 1981; 13:299-309. [PMID: 6455329 DOI: 10.1016/0378-1119(81)90034-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The pHA10 plasmid was designed for the cloning and selection of transcriptional termination signals. This study demonstrates the use of pHA10 as a cloning vehicle in the selection and characterization of an N-unresponsive terminator. Following the random cloning of lambda DNA, and N-unresponsive transcription terminator was isolated. Hybridization of in vivo 32P-labeled RNA to various DNA fragments, using the Southern (1975) blotting technique, revealed that the transcriptional barrier that cannot be overridden in the presence of N is located close to the end of gene J of lambda DNA. The terminator determines the 3'-end of the pL operon and prevents the transcription of the anti-sense DNA strand of lambda late genes. The primary structure and other characteristics of this terminator are now under investigation.
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14
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Kumar SA. The structure and mechanism of action of bacterial DNA-dependent RNA polymerase. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1981; 38:165-210. [PMID: 6170089 DOI: 10.1016/0079-6107(81)90013-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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15
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Rosenvold EC, Calva E, Burgess RR, Szybalski W. In vitro transcription from the b2 region of bacteriophage lambda. Virology 1980; 107:476-87. [PMID: 6450480 DOI: 10.1016/0042-6822(80)90314-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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16
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Calva E, Burgess R. Characterization of a rho-dependent termination site within the cro gene of bacteriophage lambda. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)70409-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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17
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Calva E, Rosenvold E, Szybalski W, Burgess R. Analysis of the in vitro synthesis of 5'-gamma-32P-labeled transcripts from coliphage lambda by gel electrophoresis, RNA-DNA hybridization, and RNase T1 digestion. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)70408-6] [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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18
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Schechtman MG, Alegre JN, Roberts JW. Assay and characterization of late gene regulators of bacteriophages lambda82 and phi.. J Mol Biol 1980; 142:269-88. [PMID: 6450836 DOI: 10.1016/0022-2836(80)90273-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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19
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Schechtman MG, Snedeker JD, Roberts JW. Genetics and structure of the late gene regulatory region of phage 82. Virology 1980; 105:393-404. [PMID: 6448512 DOI: 10.1016/0042-6822(80)90040-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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20
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Gottesman ME, Adhya S, Das A. Transcription antitermination by bacteriophage lambda N gene product. J Mol Biol 1980; 140:57-75. [PMID: 6447798 DOI: 10.1016/0022-2836(80)90356-3] [Citation(s) in RCA: 181] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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21
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Abstract
The regulatory effects of host cellular histones on the transcription of simian virus 40 (SV40) DNA were investigated by using reconstituted and native SV40 nucleoprotein complexes (NPCs). Reconstituted NPCs were prepared from SV40 DNA and the combination fraction of five histones, H1, H2A, H2B, H3, and H4, isolated from the nuclei of permissive (CV-1) or nonpermissive (BALB/c 3T3, rat liver, and calf thymus) cells. Native NPCs were prepared by alkali disruption of purified SV40 virions. Nuclease digestion of these NPCs gave regular patterns of bands similar to those of SV40 NPCs from SV40-infected CV-1 cells, suggesting the presence of a nucleosomal structure. Transcription of NPCs was analyzed in vitro by using Escherichia coli DNA-dependent RNA polymerase. Both histone H1 and the fraction consisting of all five histones inhibited transcription of SV40 DNA by about 90 to 95%. The fraction consisting of four histones lacking H1 reduced the transcription by 30 to 35%, to a level similar to that of transcription with native NPCs. Transcription was inhibited regardless of whether the origin of histones was permissive or nonpermissive cells. Gel electrophoretic patterns of RNA products transcribed from SV40 DNA and reconstituted and native NPCs showed several identical peaks between 13S and 28S. The patterns were identical whether NPCs reconstituted with H1 alone, all five histones, or four histones lacking H1 were used.
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22
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Chiang T, Roessner C, Ihler G. Location of ribosome binding sites on the right end of lambda DNA. J Mol Biol 1979; 135:893-906. [PMID: 161332 DOI: 10.1016/0022-2836(79)90518-7] [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: 12/13/2022]
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23
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24
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Abstract
Physical and genetic mapping of deletion mutations has been correlated with the available molecular sizes of the lambda gene products and the DNA base sequence to construct a comprehensive molecular map of the phage lambda genome. The physical length of the DNA making up the left arm from the cos site through gene J is not sufficient to account in a nonoverlapping manner for all the proteins of the sizes reported to be coded, especially in the Nu1--C region. In the right arm all the coding capacity has not been accounted for, and it appears to be oversaturated only in the gam-ral region. The positions of several IS and Tn elements, and of restriction endonuclease cleavage sites are specified.
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25
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Taylor WE, Burgess RR. Escherichia coli RNA polymerase binding and initiation of transcription on fragments of lambda rifd 18 DNA containing promoters for lambda genes and for rrnB, tufB, rplC,A, rplJ,L, and rpoB,C genes. Gene 1979; 6:331-65. [PMID: 159206 DOI: 10.1016/0378-1119(79)90073-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Promoters of genes for bacteriophage lambda and for Escherichia coli ribosomal RNA (rrnB), elongation factor Tu (tufB), ribosomal proteins L11 (rplK), L1 (rplA), L10 (rplJ), and L7/L12 (rplL), and RNA polymerase subunits beta (rpoB) and beta' (rpoC) were studied by use of two types of filter binding assays which measured E. coli RNA polymerase binding and initiation of transcription on restriction fragments of lambda rifd 18 DNA. The DNA fragments selectively retained on filters were eluted, concentrated, and analyzed by gel electrophoresis. The binding characteristics of these promotor fragments were qualitatively determined by varying the RNA polymerase, salt, and glycerol concentrations in the polymerase binding assay with HaeIII fragments of lambda rifd 18 DNA. The approximate map locations of these small HaeIII fragments were determined by HaeIII digestion of the larger, previously mapped EcoRI, HindIII, and SmaI restriction fragments of the phage DNA. The base compositions proximal to the 5' ends of mRNA's from promoters on these DNA fragments were elucidated by the polymerase initiation assay, in which the addition of various combinations of nucleoside triphosphates to the reaction allowed RNA polymerase to form high-salt-resistant initiation complexes with some of the known SmaI + EcoRI, EcoRI + HindIII, or HaeIII restriction fragments of lambda rifd 18 DNA. The data obtained by this technique are consistent with the map positions and 5' mRNA base sequences of the known lambda promotors p'R, po, pR and pL. In the main focus of this work, we have determined the approximate map locations and 5' mRNA base compositions of several promoters for known E. coli genes including rrnB, tufB, rplK,A, and rplJ,L. No promoter was detected between rplL and the rpoB,C genes. Thus our data are consistent with the conclusion of Yamamoto and Nomura (1978) that the beta and beta' mRNA is probably cotranscribed from the promoter for rplJ,L. Finally, the approximate map positions and the NTP combinations which initiated transcription of several unknown lambda and E. coli in vitro promoters are reported. The methods reported should prove useful for studying the characteristics of promoters on other cloned DNA regions.
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28
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Sahagan BG, Dahlberg JE. A small, unstable RNA molecule of Escherichia coli: spot 42 RNA. I. Nucleotide sequence analysis. J Mol Biol 1979; 131:573-92. [PMID: 390161 DOI: 10.1016/0022-2836(79)90008-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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29
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Sahagan BG, Dahlberg JE. A small, unstable RNA molecule of Escherichia coli: spot 42 RNA. II. Accumulation and distribution. J Mol Biol 1979; 131:593-605. [PMID: 229230 DOI: 10.1016/0022-2836(79)90009-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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30
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Morita M, Oka A. The structure of a transcriptional unit on colicin E1 plasmid. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 97:435-43. [PMID: 380993 DOI: 10.1111/j.1432-1033.1979.tb13131.x] [Citation(s) in RCA: 131] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In an RNA-synthesizing system in vitro, a low-molecular-weight RNA consisting of about 110 residues (RNA-I) was efficiently synthesized on DNA of colicin E 1 plasmid (ColE1) and its deletion derivatives. The promoter site for RNA-I was analysed by testing the RNA polymerase-binding ability and template activity of restriction fragments; it was mapped in the region between the replication initiation site and the colicin immunity gene of ColE1. The direction of transcription was determined by hybridization tests to the separated strands of the template. The DNA region directing RNA-I was sequenced, and RNA-I was assigned on the sequence based on the nearest-neighbour data of RNA. The sequences of its promoter and terminator regions were also deduced. Although the function of this small RNA species is unknown, a unique secondary structure could be constructed from its sequence and sensitivity to RNase.
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31
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Hamada H, Muramatsu M, Urano Y, Onishi T, Kominami R. In vitro synthesis of a 5S RNA precursor by isolated nuclei of rat liver and HeLa cells. Cell 1979; 17:163-73. [PMID: 110459 DOI: 10.1016/0092-8674(79)90304-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Isolated rat liver nuclei were incubated under appropriate conditions in the presence of 0.5 micrograms/ml alpha-amanitin and an RNAase inhibitor prepared from cytosol fraction, together with alpha-32P-UTP or alpha-32P-CTP and three other nucleoside triphosphates. RNA extracted by an SDS-hot phenol procedure was fractionated with sucrose density gradient centrifugation followed by acrylamide gel electrophoresis. Fingerprint analysis of the in vitro synthesized "5S" RNA, which was slightly larger than mature 5S RNA on gel electrophoresis, showed that it contained all the sequences of mature 5S RNA except for the oligonucleotide at the 3' end. Instead, it contained two additional spots which were not present in mature 5S RNA. Analysis of the extra spots revealed that they were derived from the 3' end of the in vitro synthesized "5S RNA, which were sequenced tentatively as -CUUGAUGCUUoh (extra sequence underlined). The 5' end of the product was (p)pGU--. Isolated HeLa cell nuclei synthesized similar sized "5S" RNA under the same conditions. We conclude from these results that in isolated nuclei of these mammalian cells RNA polymerase III starts transcription of 5S RNA gene at the same site as the 5' end of mature 5S RNA, proceeds toward the 3' direction and stops at a site probably 8 nucleotides downstream from the 3' end of mature 5S RNA. Experiments with a short pulse and with various "chases" have demonstrated the presence of a short-lived precursor 5S RNA which is similar in size and sequence to in vitro "5S" RNA, suggesting that 5S RNA is synthesized in vivo as a longer precursor molecular as demonstrated in this in vitro system, and is rapidly processed into mature 5S RNA.
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Hoflack B, D'Halluin JC, Popic S, Nicholson G, Krsmanovic V. A thermal sensitive function of KB cell DNA-dependent RNA polymerase IB involved in RNA chain growth. Biochimie 1979; 60:1187-91. [PMID: 737198 DOI: 10.1016/s0300-9084(79)80354-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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34
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Gutai MW, Nathans D. Evolutionary variants of simian virus 40: Nucleotide sequence of a conserved SV40 DNA segment containing the origin of viral DNA replication as an inverted repetition. J Mol Biol 1978; 126:259-74. [PMID: 216810 DOI: 10.1016/0022-2836(78)90362-5] [Citation(s) in RCA: 64] [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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36
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Abstract
The 5,577 nucleotide long sequence of bacteriophage G4 DNA has been determined using the 'plus and minus' and chain termination methods of DNA sequencing. This sequence has been compared with that of the closely related bacteriophage phiX174 (refs 1, 55). In the coding regions there is an average of 33.1% nucleotide sequence differences between the two genomes, but the distribution of these changes is not random and the sequence of some genes is more conserved than others. There is less sequence similarity between the untranslated intergenic regions of G4 and phiX174, but despite this the sequences of the J/F, F/G and H/A untranslated spaces in both genomes have similar sized hairpin loops, which may be related to their function.
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37
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Bastia D. Determination of restriction sites and the nucleotide sequence surrounding the relaxation site of ColE1. J Mol Biol 1978; 124:601-39. [PMID: 712849 DOI: 10.1016/0022-2836(78)90174-2] [Citation(s) in RCA: 63] [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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38
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Salstrom JS, Szybalski W. Coliphage lambdanutL-: a unique class of mutants defective in the site of gene N product utilization for antitermination of leftward transcription. J Mol Biol 1978; 124:195-221. [PMID: 361968 DOI: 10.1016/0022-2836(78)90156-0] [Citation(s) in RCA: 183] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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39
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Harris B, Roeder R. Structural relationships of low molecular weight viral RNAs synthesized by RNA polymerase III in nuclei from adenovirus 2-infected cells. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(17)34692-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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40
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van Heuverswyn H, van de Voorde A, Fiers W. Nucleotide sequence of the simian-virus-40 DNA region coding for the carboxyl-terminal part of the T antigen. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 86:335-44. [PMID: 207522 DOI: 10.1111/j.1432-1033.1978.tb12315.x] [Citation(s) in RCA: 11] [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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41
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Lee F, Bertrand K, Bennett G, Yanofsky C. Comparison of the nucleotide sequences of the initial transcribed regions of the tryptophan operons of Escherichia coli and Salmonella typhimurium. J Mol Biol 1978; 121:193-217. [PMID: 351195 DOI: 10.1016/s0022-2836(78)80005-9] [Citation(s) in RCA: 82] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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42
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Termination of transcription by Escherichia coli RNA polymerase in vitro is affected by ribonucleoside triphosphate base analogs. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(17)38094-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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43
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Küpper H, Sekiya T, Rosenberg M, Egan J, Landy A. A rho-dependent termination site in the gene coding for tyrosine tRNA su3 of Escherichia coli. Nature 1978; 272:423-8. [PMID: 345126 PMCID: PMC1994828 DOI: 10.1038/272423a0] [Citation(s) in RCA: 111] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A set of partially overlapping DNA restriction fragments that support promoter-dependent transcription of the tRNATyr1 gene of Escherichia coli has been used to study site-specific termination in vitro. Transcription termination occurs at a specific site 224-226 nucleotides beyond the end of the structural gene and is completely dependent on rho-factor. Certain features of this site suggest differences from other termination sites previously studied. A role for specific sequence recognition is suggested.
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44
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Rosenberg M, Court D, Shimatake H, Brady C, Wulff DL. The relationship between function and DNA sequence in an intercistronic regulatory region in phage lambda. Nature 1978; 272:414-23. [PMID: 634366 DOI: 10.1038/272414a0] [Citation(s) in RCA: 310] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
rho factor-mediated transcription termination at the tr1 terminator site of bacteriophage lambda is examined. Mutations affecting the termination event are characterised. These mutations define features of the site which seem to be important to terminator function. In addition, other related transcriptional and translational regulatory elements are defined within the region surrounding the termination site. The potential molecular interactions and structural overlaps of these control signals apparently couple the regulation of the decision between lytic and lysogenic growth patterns by phage lambda.
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45
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Nucleotide sequence of DNA template for the 3' ends of SV40 mRNA. II. The sequence of the DNA fragment EcorII-F and a part of EcorII-H. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(17)34909-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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46
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Dhar R, Lai CJ, Khoury G. Nucleotide sequence of the DNA replication origin for human papovavirus BKV: sequence and structural homology with SV40. Cell 1978; 13:345-58. [PMID: 203403 DOI: 10.1016/0092-8674(78)90203-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA and RNA sequencing techniques were used to obtain the sequence surrounding the origin of DNA replication for human papovavirus BKV. The structure is characterized by a true palindrome of 17 residues followed by two sets of symmetrical sequences and a stretch of 20 AT residues. Within the two symmetrical sequences is a segment containing a strong purine bias, 23 of 26 nucleotides. These structures are similar, if not identical, to those found in the region of the SV40 replication, origin. Within the homologous DNA segments, 60-80% of the BKV and SV40 nucleotides are the same. The remarkable similarity of BKV and SV40 sequences containing the origins of DNA replication would appear to confirm our previous suggestion of an evolutionary relationship between the two genomes. In addition, topological similarities between these sequences suggest the possibility of certain structural requirements for bidirectional replication origins in these superhelical DNAs.
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48
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Nucleotide sequence of the DNA encoding the 5'-terminal sequences of simian virus 40 late mRNA. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(17)38252-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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49
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THE ROLE OF RHO IN TRANSCRIPTION TERMINATION IN E. COLI. Gene Expr 1978. [DOI: 10.1016/b978-0-08-022624-8.50023-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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50
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Jacq B, Jourdan R, Jordan BR. Structure and processing of precursor 5 S RNA in Drosophila melanogaster. J Mol Biol 1977; 117:785-95. [PMID: 416221 DOI: 10.1016/0022-2836(77)90069-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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