Termination of transcription in bacteriophage lambda. Heterogeneous, 3'-terminal oligo-adenylate additions and the effects of rho factor

Consensus architecture of promoters and transcription units in Escherichia coli: design principles for synthetic biology

Genetic information in genomes is ordered, arranged in such a way that it constitutes a code, the so-called cis regulatory code. The regulatory machinery of the cell, termed trans-factors, decodes and expresses this information. In this way, genomes maintain a potential repertoire of genetic programs, parts of which are executed depending on the presence of active regulators in each condition. These genetic programs, executed by the regulatory machinery, have functional units in the genome delimited by punctuation-like marks. In genetic terms, these informational phrases correspond to transcription units, which are the minimal genetic information expressed consistently from initiation to termination marks. Between the start and final punctuation marks, additional marks are present that are read by the transcriptional and translational machineries. In this work, we look at all the experimentally described and predicted genetic elements in the bacterium Escherichia coli K-12 MG1655 and define a comprehensive architectural organization of transcription units to reveal the natural genome-design and to guide the construction of synthetic genetic programs.

Bacteriophage T7 mRNA is polyadenylated

To determine whether the RNA of bacterial viruses is polyadenylated like bacterial mRNAs, pulse-labelled as well as the steady-state population of bacteriophage T7-specific transcripts were examined for the presence of poly(A) tracts by binding to oligo(dT) cellulose followed by hybridization with specific gene probes. Representatives of all classes of bacteriophage-specific mRNA--early, middle and late--were found to be polyadenylated. This conclusion was confirmed by screening the products of oligo(dT)-dependent cDNA synthesis. A cDNA library was prepared from RNA synthesized after bacteriophage T7 infection and the sequence of bacteriophage-specific clones was determined to define the sites of polyadenylation. About half of the clones were polyadenylated near the end of a protein-coding region, one of them at the site of post-transcriptional processing by RNase III. Other clones were polyadenylated within protein-coding regions. These observations suggest that polyadenylation occurs after the nucleolytic processing of primary transcripts and in some cases also after mRNA degradation has already begun.

Regulation of the elongation-termination decision at intrinsic terminators by antitermination protein N of phage lambda

The mechanisms that control N-protein-dependent antitermination in the phage lambda life cycle have counterparts in the regulatory systems of other organisms. Here we examine N-dependent antitermination at the intrinsic tR' terminator of lambda to elucidate the regulatory principles involved. The tR' terminator consists of a sequence of six base-pairs along the template at which the transcription complex is sufficiently destabilized to make RNA release possible. Within this "zone of opportunity" for termination the termination efficiency (TE) at each template position is determined by a kinetic competition between alternative reaction pathways that lead either to elongation or to termination. TE values at each position within tR' have been mapped as a function of NTP concentration, and it is shown that N protein (in the presence of NusA and a nut site; the minimal system for N-dependent antitermination) can offset increases in TE that are induced by limiting the concentrations of each of the next required NTPs. By limiting NTP concentrations or working at low temperature we show that a significant effect of N within the minimal system is to increase the rate of transcript elongation three- to fivefold at most positions along the template. Assuming that a comparable increase in elongation rate applies at template positions within the terminator, we show that an increase of this magnitude is not sufficient to account for the antitermination efficiency observed and that an approximately 100-fold stabilization of the transcription complex at intrinsic termination sites as a consequence of binding the N-containing antitermination sub-assembly must be invoked as well. A general method for partitioning TE effects in antitermination between changes in elongation rate and termination complex stability is demonstrated, based on competing free energy of activation barriers for the elongation and termination reactions. The analysis and utility of such mixed modes of transcriptional regulation are considered in general terms.

Polyadenylation of mRNA in prokaryotes

The 3'-ends of both prokaryotic and eukaryotic mRNA are polyadenylated, but the poly(A) tracts of prokaryotic mRNA are generally shorter, ranging from 15 to 60 adenylate residues and associated with only 2-60% of the molecules of a given mRNA species. The sites of polyadenylation of bacterial mRNA are diverse and include the 3'-ends of primary transcripts, the sites of endonucleolytic processing in the 3' untranslated and intercistronic regions, and sites within the coding regions of mRNA degradation products. The diversity of polyadenylation sites suggests that mRNA polyadenylation in prokaryotes is a relatively indiscriminate process that can occur at all mRNA's 3'-ends and does not require specific consensus sequences as in eukaryotes. Two poly(A) polymerases have been identified in Escherichia coli. They are encoded by unlinked genes, neither of which is essential for growth, suggesting significant functional overlap. Polyadenylation promotes the degradation of a regulatory RNA that inhibits the replication of bacterial plasmids and may play a similar role in the degradation of mRNA. However, under certain conditions, poly(A) tracts may lead to mRNA stabilization. Their ability to bind S1 ribosomal protein suggests that poly(A) tracts may also play a role in mRNA translation.

Studying promoters and terminators by gene fusion

Prokaryotic gene control signals can be isolated, compared, and characterized by precise fusion in vitro to the Escherichia coli galactokinase gene (galK), which provides both a simple assay and genetic selection. This recombinant galK fusion vector system was applied to the study of promoters and terminators recognized by the Escherichia coli RNA polymerase. Three promoters created by mutation from DNA sequences having no promoter function were characterized. Mutations that inactivate promoter function were selected, structurally defined, and functionally analyzed. Similarly, transcription termination was examined, and mutations affecting terminator function were isolated and characterized.

The tL2 cluster of transcription termination sites between genes bet and ral of coliphage lambda

The major leftward transcription of bacteriophage lambda is controlled by several terminators (t), including tL1, tL2, tL3, and others. The tL2 termination site, which was placed by Salstrom and Szybalski (Virology 88, 252-260, 1978) between lambda genes bet and ral, was found to consist of a cluster of four leftward terminators. As not to change the numbering of other leftward terminators, these were designated as tL2a, tL2b, tL2c, and tL2d. As determined by S1 nuclease mapping of the tL2-terminated in vitro transcripts, the normally pL-initiated major leftward lambda transcription should encounter termination points at 1653 bp (tL2a; between genes Ea10 and ral), 2089 bp (tL2b; between genes cIII and Ea10), 2441-2442 bp, and 2483 bp (tL2c and tL2d; both within gene gam) from the sL startpoint (= +1). All terminators were cloned in a pBR322-derived plasmid between the p'R promoter and the galK gene, and their in vivo termination efficiencies are 69% (tL2a), 53% (tL2b), and 38% (tL2c + tL2d), measured as reduction of galK expression in rho+galK- hosts at 30 degrees. The tL2a and tL2b), terminators depend little on the rho factor, whereas the efficiency of tL2c + tL2d decreases from 38 to only 14% in the rho- host. When shifted to 42 degrees, the termination efficiency of tL2b decreases from 53 to only 36%, while the other tL2 terminators are much less affected by increasing the temperature. The calculated joint efficiency of the entire tL2 cluster is 90%, which is in perfect agreement with the 90% termination efficiency reported by Salstrom and Szybalski (1978) for tL2. However, the natural location of tL2c and tL2d within the actively translated gam gene may interfere with their termination function. Under in vitro conditions, tL2c and tL2d are active only in the presence of rho factor, whereas tL2a and tL2b do not require rho. The structure of the tL2 terminators resembles that of some other known termination sites: a perfect (8 bp for tL2a and tL2b) or imperfect (8-9 bp) dyad symmetry and a T6 (tL2a), T5 (tL2b), T4 (tL2c) or TTATT sequence (tL2d) toward the 3' end of the mRNA-like DNA strand.

A cluster of leftward, rho-dependent t'J terminators in the J gene of coliphage lambda

While searching for the N-unresponsive terminator described by Honigman (Gene 13 (1981) 299-309), a 1680-bp DNA fragment from within gene J of bacteriophage lambda was cloned into plasmid pD12 between promoter p'R and the galK gene. In vitro transcription of this plasmid and S1 mapping assays, together with nucleotide sequencing, demonstrated that this DNA fragment contains a cluster of at least four in rho+ Escherichia coli hosts and only 30% in rho- hosts at at 30 degrees C. At the elevated temperature of 42 degrees C, the rho-dependent termination component of the t'J cluster becomes somewhat leaky, with the readthrough increasing by about twofold. The t'J terminators appear to be less responsive to nutR- and N-mediated antitermination (efficiency of 84-87%) than tL3, which responds to the same antitermination function with an efficiency of 97%. The relationship between the t'J cluster and the same antitermination function with an efficiency of 97%. The relationship between the t'J cluster and the highly N-unresponsive leftward termination signal tJ, which is also located within the J gene region (Gottesman et al., J. Mol. Biol. 140 (1980) 57-75; Honigman, Gene 13 (1981) 299-309), is unknown.

Tandem transcription-termination sites in the late rightward operon of bacteriophage lambda

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.

Quantitative estimate of unlabelled cordycepin in acid-soluble pool isolated from rat brain tissue after intraperitoneal injection of the inhibitor

A technique for the quantitative estimation of intraperitoneally injected unlabelled cordycepin in an acid-soluble pool (ASP) isolated from rat brain tissue is suggested. It consists in consecutive chromatography of ASP on Dowex 1 X 8, Dihydroxyboryl = SP500 and Sephasorb-HP. The fraction containing 2'-deoxyriboadenosine and 3'-deoxyriboadenosine (cordycepin) has been isolated from brain tissue ASP of experimental animals after a cordycepin injection. 2'-Deoxyriboadenosine fraction has been isolated from tissue ASP of the control animals not subjected to an inhibitor injection. Brain tissue antibiotic content has been estimated by the difference in nucleoside quantity values (microM) in these two fractions (control/experiment).

Purified lambda regulatory protein cII positively activates promoters for lysogenic development

The bacteriophage lambda regulatory protein, cII, has been purified and shown to activate positively RNA transcription from the two phage promoters which coordinately regulate phage lysogenic development. To obtain this protein, the cII gene was cloned into a plasmid vector carrying the strong, regulatable lambda phage promoter PL such that it was overproduced to levels approaching 5% of cellular protein.

Pausing of RNA polymerase during in vitro transcription of the tryptophan operon leader region

RNA polymerase molecules pause at a single site during in vitro transcription of the tryptophan (trp) operon leader region. Pausing was observed when DNA templates derived from Escherichia coli. Salmonella typhimurium, and Klebsiella aerogenes were used. Fingerprint analyses showed that the major RNA species produced by the transcriptional pause is 91 nucleotides long. A minor RNA species 90 nucleotides long was also detected. Single-round transcription experiments were used to study the kinetics of pausing. Time course, pulse-chase, and delayed-labeling experiments suggest that every RNA polymerase molecule transcribing the trp leader region pauses. A suboptimal ribonucleoside triphosphate concentrations, the half-life of paused-leader RNA was approximately 3 min at 22 degrees C and 0.7 min at 37 degrees C. At near-optimal ribonucleoside triphosphate concentrations, the half-time of the paused species dropped to about 0.3 min at 22 degrees C. The appearance and half-life of the paused species were unaffected by salt concentration, rho factor, guanosine 3'-5'-bis(diphosphate), or point mutations in the trp attenuator region. It is postulated that transcriptional pausing may play a role in maintaining the synchronization of transcription and translation that is vital in the control of transcription termination at the trp operon attenuator.

A comprehensive molecular map of bacteriophage lambda

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.

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

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.

Efficient cap-dependent translation of polycistronic prokaryotic mRNAs is restricted to the first gene in the operon

Certain polycistronic prokaryotic mRNAs, when modified at their 5'-termini with a cap structure, are translated as efficiently as, or more efficiently than eukaryotic mRNAs in a eukaryotic cell-free protein synthesising system. However, in this case efficient cap-dependent translation is apparently restricted to the 5'-proximal coding sequence. Moreover, certain translational regulatory signals potentially used by these prokaryotic mRNAs to regulate their levels of expression seem to be recognised by the eukaryotic translational components. The evolutionary significance and practical implications of these results are discussed.

Efficient translation of prokaryotic mRNAs in a eukaryotic cell-free system requires addition of a cap structure

In this and the accompanying paper we demonstrate that certain prokaryotic mRNAs, when modified at their 5'-termini with a cap structure, are translated in a eukaryotic cell-free protein synthesising system as efficiently as, or more efficiently than, eukaryotic mRNAs. Apparently, the prokaryotic mRNA contains all the information necessary for efficient recognition and initiation by eukaryotic translational components, except for the cap structure.

Nucleotide sequence of Xenopus borealis oocyte 5S DNA: comparison of sequences that flank several related eucaryotic genes

Genomic Xenopus borealis oocyte-specific 5S DNA (Xbo) contains clusters of 5S rRNA genes. The number of genes varies among clusters, and the distance between genes within a cluster is about 80 nucleotides. The spacer DNA between gene clusters is AT-rich and heterogeneous in length due in part to variable numbers of a tandemly repeated 21 nucleotide sequence. A cloned fragment of Xbo 5S DNA (Xbo1) containing three 5S rRNA genes has been sequenced. The sequences of Xbo1 genes 1 and 2 are very similar to the dominant 5S RNA sequence, whereas 15 of the 120 residues in the third gene are different. The sequence of gene 3 is as different from the dominant gene sequence as the X. laevis pseudogene is from the 5S RNA gene. Sequence analysis of genomic DNA shows that gene 3 is an abundant component of the multigene family. All three genes are transcribed when added to an extract of X. laevis oocyte nuclei, and a fragment of Xbo1 lacking the AT-rich spacer DNA and the 5' end of the first gene supports transcription of genes 2 and 3 in this in vitro system. Thus the 80 nucleotides preceding each 5S gene are sufficient for promoter function. Nucleic acid sequences preceding several eucaryotic genes that are transcribed by RNA polymerase III were analyzed and the following common features were found: a purine-rich region; at least one direct repeat; the absence of dyad symmetry; transcription beginning with a purine; a pyrimidine residue immediately preceding the first nucleotide of the gene; and the oligonucleotides AAAAG, AGAAG and GAC, located approximately 15, 25 and 35 nucleotides, respectively, before the start of transcription. The 10 base pair (bp) spacing between the homologous oligonucleotides is that expected for a recognition signal on one face of a DNA double helix. The extensive sequence differences between most of the spacers that precedes these genes make the three conserved oligonucleotides more striking. Parts of the 5' flanking regions of the three Xbo1 gene (-12 to -40), which include the conserved oligonucleotides, are identical. In contrast, 7 of the first 11 nucleotides that precede the third 5S RNA gene in Xbo1 differ from those that precede the first gene. The sequences following the X. borealis oocyte and somatic 5S genes are identical in 12 of the first 14 residues and contain two or more T clusters, as does the corresponding region of X. laevis oocyte 5S DNA. The 3' sequences of the Xenopus 5S rRNA genes and several other eucaryotic genes contain features in common with procaryotic transcription termination sites. The 3' end of the gene is GC-rich and contains a dyad symmetry. Termination occurs in an AT-rich region containing one or more T clusters on the noncoding strand.

Highly reiterated sequences of SIMIANSIMIANSIMIANSIMIANSIMIAN

A 172-base pair segment of DNA that is repeated several million times in the genome of the African green monkey has been characterized. Sequence analysis revealed that the many repeats of this complex unit are not all identical but represent a set of closely related segments: Sequence divergence occurs at various positions in the segment in a nonrandom manner. The uncloned segment obtained from monkey DNA is compared with a cloned segment of the same DNA which was recombined into the genome of simian virus 40 during permissive infection.

A rho-dependent termination site in the gene coding for tyrosine tRNA su3 of Escherichia coli

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.

The relationship between function and DNA sequence in an intercistronic regulatory region in phage lambda

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.

Nucleotide sequence of the DNA replication origin for human papovavirus BKV: sequence and structural homology with SV40

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.

Bacteria with defective rho factors suppress the effects of N mutations in bacteriophage lambda

A prediction based on the model for N-gene function of bacteriophage lambda proposed by Roberts (1971) is confirmed by showing that a lambdaN- double mutant is able to grow in strains of E. coli with defective rho transcription termination factors. The burst sizes for lambdaN- in these strains range from 5 to 24% the burst sizes for lambdaN+ in the same strain. This low level of suppression is also evident in the levels of synthesis of the lambda exonuclease and is consistent with other evidence that the defect in the rho factors of these strains is only partial. These strains do not suppress the effects of mutations in genes O, P and Q of lambda nor in genes 30 and 43 of bacteriophage T4. The lack of suppression of lambdaQ- is significant because the Q-gene product, like the N-gene product, is believed to function as an anti-terminator of lambda transcription but at termination sites that may not require rho factor action.

In situ hybridization of repetitive monkey genome sequences isolated from defective simian virus 40 DNA

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.

4S oop RNA is a leader sequence for the immunity-establishment transcription in coliphage lambda

oop RNA, which is initiated at the po promoter and is 81 nucleotides long, can function as a leader sequence for the lambda immunity establishment transcription, previously believed to originate at a special promoter pre located in the y region. Thus, oop RNA seems to have a dual role, either favouring the lytic cycle as a primer for the initiation of lambda DNA replication, or leading to the establishment of lysogeny when elongated into the imm transcript, which directs synthesis of the repressor.

SV40 DNA sequences as an example of the structure of genes functioning in animal cell nuclei

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.