Attenuation and processing of RNA from the rplJL--rpoBC transcription unit of Escherichia coli

Transcription mapping of the Escherichia coli chromosome by electron microscopy

The distinctive double Christmas tree morphology of rRNA operons as visualized by electron microscopy makes them easy to recognize in chromatin spreads from Escherichia coli. On the basis of the pattern of nascent transcripts on nearby transcription units and the relative distances of the operons from one another and the replication origin, we are now able to specifically identify five of the seven rRNA operons in E. coli. The use of rRNA operons as markers of both position and distance has resulted in the morphological mapping of a significant portion of the E. coli chromosome; over 600 kilobase pairs in the 84- to 90-min and 72-min regions can now be recognized. Since individual rRNA operons could be identified, direct comparisons could be made of their transcriptional activities. As judged by the densities of RNA polymerases along the operons, rrnA, rrnB, rrnC, rrnD, and rrnE were all transcribed at similar levels, with one RNA polymerase every 85 base pairs. The ability to recognize individual operons and specific regions of the chromosome allows direct comparisons of various genetic parameters.

SecA protein autogenously represses its own translation during normal protein secretion in Escherichia coli

The Escherichia coli secA gene, whose expression is responsive to the protein secretion status of the cell, is the second gene in an operon. We found that both the basal and induced levels of SecA biosynthesis are dependent on prior translation of the upstream gene, gene X, and identified two large gene X-secA transcripts. The 10-fold derepression of secA expression by protein export defects was at the translational level since no further increases in gene X or secA mRNA levels were detected during this period, and a secA-lacZ protein fusion but not an operon fusion was appropriately derepressed. Furthermore, overexpression of the SecA protein severely reduced expression of only the secA-lacZ protein fusion, indicating that SecA autogenously represses its own translation.

Retroregulation of the bacteriophage lambda int gene: limited secondary degradation of the RNase III-processed transcript

Expression of the int gene of bacteriophage lambda from two promoters, pI and pL, is differentially regulated through RNA processing. Efficient Int protein synthesis from the pL RNA is inhibited by the action of sib, a cis-acting retroregulator downstream from the int gene. We have used mapping procedures with nuclease S1 to study the pL transcripts produced in vivo after phage lambda infection. We have found an RNase III-dependent processing site within the Int coding sequence, 387 nucleotides upstream from the site of the primary cleavage by RNase III at Sib. This secondary processing site is located at the most stable region of secondary structure in the sib int region, as predicted by computer analysis. We suggest that RNase III cleavage at the Sib site allows processive exonucleolytic degradation of the RNA to proceed to a region of secondary structure within the Int coding sequence, which protects the upstream region of the transcript from further degradation.

Stabilization of discrete mRNA breakdown products in ams pnp rnb multiple mutants of Escherichia coli K-12

The degradation of mRNA in Escherichia coli is thought to occur through a series of endonucleolytic and exonucleolytic steps. By constructing a series of multiple mutants containing the pnp-7 (polynucleotide phosphorylase), rnb-500 (RNase II), and ams-1 (altered message stability) alleles, it was possible to study general mRNA turnover as well as the degradation of specific mRNAs. Of most interest was the ams-1 pnp-7 rnb-500 triple mutant in which the half-life of total pulse-labeled RNA increased three- to fourfold at the nonpermissive temperature. RNA-DNA hybridization analysis of several specific mRNAs such as trxA (thioredoxin), ssb (single-stranded-DNA-binding protein), uvrD (DNA helicase II), cat (chloramphenicol acetyltransferase), nusA (N utilization substance), and pnp (polynucleotide phosphorylase) demonstrated two- to fourfold increases in their chemical half-lives. A new method for high-resolution Northern (RNA) analysis showed that the trxA and cat mRNAs are degraded into discrete fragments which are significantly stabilized only in the triple mutant. A model for mRNA turnover is discussed.

Complete nucleotide sequence of the ribosomal 'A' protein operon from the archaebacterium, Halobacterium halobium

DNA fragments cloned from the halophilic archaebacterium Halobacterium halobium including the gene for ribosomal 'A' protein (HhaL20) were sequenced. Sequence and transcript analyzes indicated that the 'A' protein message (ORFC) was co-transcribed with two neighbouring open reading frames (ORFA and B) as a single unit. Comparison of the amino acid sequences deduced from ORFA and B with those from other organisms demonstrated that ORFA encoded the protein homologous to the ribosomal protein L8 of Halobacterium cutirubrum (HcuL8) and L1 of Escherichia coli (EL1), while ORFB encoded the protein homologous with the human ribosomal protein P0. The sequences which were able to facilitate mRNA.16S-rRNA hybridization were found about 10-20 nucleotides upstream of the initiation codon ATG of each of the three ORFs. The 5'- and 3'-ends of the operon were mapped with nuclease S1. A putative promoter (A+T-rich) and termination signal (T-rich) were found to be present within the 5'- and 3'-flanking sequence.

Alternative promoters in the development of bacteriophage plasmid P4

Infection of Escherichia coli with the satellite virus P4 without its helper bacteriophage P2 leads either to the immune integrated state or to the nonimmune multicopy plasmid condition. We analyzed the transcription pattern of the phage plasmid P4 early and late after infection and during the stable plasmid or lysogenic condition. The early postinfection phase is characterized by the leftward transcription of an operon including the genes cI (P4 immunity) and alpha (replication). This early transcript starts from the promoter PLE, which shows a good homology with the E. coli sigma 70 promoter. At later times, the transcription of this operon starts from a different promoter, PLL, located 400 base pairs upstream of PLE, and sharing little homology with the canonical E. coli promoter sequence; a longer transcript encoding an additional open reading frame is thus produced. PLL shares two boxes of homology with the P4 late promoter PSID, positively regulated by the P4 delta gene product, and depends on delta function for its full activation. In the multicopy plasmid state, the transcription pattern is similar to that observed at late times after infection. Since in the plasmid state not only is P4 immunity not expressed but its establishment is prevented, even though the P4 cI gene is transcribed, the P4 cI function may be regulated at the posttranscriptional level. In the immune state, transcription starts from PLE but does not continue to cover the P4 alpha gene. This suggests that P4 immunity acts by prematurely terminating transcription initiated at PLE.

Nucleotide sequence of the regulatory locus controlling expression of bacterial genes for bioluminescence

Production of light by the marine bacterium Vibrio fischeri and by recombinant hosts containing cloned lux genes is controlled by the density of the culture. Density-dependent regulation of lux gene expression has been shown to require a locus consisting of the luxR and luxI genes and two closely linked divergent promoters. As part of a genetic analysis to understand the regulation of bioluminescence, we have sequenced the region of DNA containing this control circuit. Open reading frames corresponding to luxR and luxI were identified; transcription start sites were defined by S1 nuclease mapping and sequences resembling promoter elements were located.

Direct evidence for rifampicin-promoted readthrough of the partial terminator tL7 in the rpoBC operon of Escherichia coli

The RNA polymerase subunits beta and beta' of Escherichia coli, encoded by the genes rpoB and rpoC, are co-transcribed with four 50 S ribosomal protein genes, rplKAJL. After treatment with the antibiotic rifampicin a partial uncoupling of rpoBC from rplKAJL transcription occurs. We have been investigating the role played in uncoupling by tL7, an 80% efficient terminator of transcription present in the 319 bp intercistronic space between rplL and rpoB, using S1 nuclease mapping of transcripts produced in vivo in normal (rpoBC haploid) strains. Our results show directly that rifampicin stimulates readthrough of tL7 on the chromosome by approximately twofold, an effect sufficient to explain the observed increase in beta beta' protein synthesis. We also provide preliminary evidence for the map position of PL7, and show that both this and P beta, two very weak promoters which might in principle be activated by rifampicin, are not in fact stimulated by the drug.

RNase III stimulates the translation of the cIII gene of bacteriophage lambda

The bacteriophage lambda cIII gene product regulates the lysogenic pathway by stabilizing the lambda cII regulatory protein. Our results show that the expression of the lambda cIII gene is subject to specific requirements. Tests of a set of cIII-lacZ gene and operon fusions reveal that a sequence upstream of the cIII ribosome binding site is needed for cIII translation. The sequence contains an inefficient RNase III processing site. Furthermore, expression of cIII is drastically reduced in cells lacking RNase III. We have isolated a phage carrying a mutation (r1), which lies in the upstream sequence, that leads to a reduction in cIII translation and inactivates the RNase III processing site. The r1 mutant is nevertheless still dependent on RNase III for cIII translation; r1 reduces cIII translation by a factor of 3 in wild-type cells and by a factor of approximately equal to 30 in an RNase III mutant host. We propose that RNase III stimulates cIII translation by binding to the upstream sequence and thereby exposing the cIII ribosome binding site. This stimulation does not involve RNA cleavage. Consistent with this hypothesis is our finding that, in vitro, unprocessed cIII mRNA is translated, whereas RNase III-cleaved cIII mRNA is not.

RNA processing by RNase III is involved in the synthesis of Escherichia coli polynucleotide phosphorylase

The synthesis of Escherichia coli polynucleotide phosphorylase (PNPase) was examined in a mutant strain defective in the RNA processing enzyme RNase III (Rnc-). We found that the specific activity and the synthesis rate of PNPase were increased in the Rnc- strain by more than three times that in an Rnc+ strain. Such increased synthesis of PNPase was not observed in a mutant strain transformed with a plasmid carrying the rnc+ gene. Quantitative analysis of RNA showed that the transcripts from the pnp gene, which encodes PNPase, were degraded more slowly in the Rnc- strain than in the Rnc+ strain. These results indicate that processing of the transcripts by RNase III is intimately involved in controlling the expression of pnp by affecting the stability of its messenger RNA.

Regulation of the promoters and transcripts of rpoH, the Escherichia coli heat shock regulatory gene

In Escherichia coli the product of the rpoH (htpR) gene, sigma 32, directs RNA polymerase to initiate transcription from heat shock promoters at all temperatures. Transcription of the heat shock genes is increased when cells are exposed to high temperatures because of increased transcription initiation by sigma 32-RNA polymerase. As a step toward understanding the regulation of the heat shock response we have examined the transcription of the rpoH gene. Using S1 mapping, promoter cloning, and in vitro transcription, we have identified the promoters and the terminator for the rpoH transcription unit. The rpoH transcripts are monocistronic and originate from at least three promoters. None of the promoters is recognized by sigma 32-RNA polymerase. Two are recognized by sigma 70-RNA polymerase and are active at both low and high growth temperatures. We do not know what form of RNA polymerase recognizes the third promoter. Transcripts from this promoter are abundant only at high temperature and are present after shift to the lethal temperature of 50 degrees C, even at times when there are no detectable transcripts from the other rpoH promoters. The amount of rpoH mRNA increases fivefold by 8 min after shift from 30 to 43.5 degrees C but rpoH mRNA synthesis increases by less than twofold, indicating that there is post-transcriptional control of the level of rpoH mRNA and presumably of sigma 32.

Evidence that Rho and NusA are involved in termination in the rplL-rpoB intercistronic region

The frequency of transcription of the ribosomal protein and RNA polymerase gene segments of the rplKAJL-rpoBC gene cluster was measured for Escherichia coli K-12 strains carrying mutations in the genes for transcriptional termination factors. The results of our study suggest that Rho increases and that both NusA and the product of sfrB decrease termination frequency in the rplL-rpoB intercistronic region.

Overproduction of DnaA protein stimulates initiation of chromosome and minichromosome replication in Escherichia coli

Increased synthesis of DnaA protein, obtained with plasmids carrying the dnaA gene controlled by the heat inducible lambda pL promoter, stimulated initiation of replication from oriC about threefold. The overinitiation was determined both as an increase in copy number of a minichromosome and as an increase in chromosomal gene dosage of oriC proximal DNA. The additional replication forks which were initiated on the chromosome did not lead to an overall increase in DNA content. DNA/DNA hybridization showed an amplification encompassing less than a few hundred kilobases on each side of oriC. Kinetic studies showed that the overinitiation occurred very rapidly after the induction, and that the initiation frequency then decreased to a near normal frequency per oriC. The results indicate that the DnaA protein is one important factor in regulation of initiation of DNA replication from oriC.

Heat shock regulatory gene rpoH mRNA level increases after heat shock in Escherichia coli

The Escherichia coli rpoH gene product sigma 32 is essential for the increase in heat shock gene transcription found after exposure of the bacteria to a sudden temperature increase. It is not known how the concentration of active sigma 32 is modulated. We showed that rpoH transcript levels increased after heat shock and that the magnitude of the increase in the level of mRNA was correlated with the magnitude of the temperature shift. The increase in the level of rpoH mRNA was still found in rpoH mutants so the mechanism of induction differed from that of the set of previously identified heat shock genes. The increased concentration of rpoH mRNA should result in a higher level of sigma 32, which is likely to be important for increasing heat shock gene transcription.

Effect of multiple copies of rpoBC on the rate of RNA synthesis in Escherichia coli

The cloning of therpoBandrpoCgenes in a high copy number vector inE. coliincreased the amount of the encoded gene products, the β and β′ subunits of RNA polymerase. However, this unexpectedly caused a 30–50% decrease in RNA synthetic activity which alternatively induced a reduction of growth rate and enlargement of cell size, and decreased the DNA replication time. The results can be explained by autogenous regulation of the RNA polymerase genes by the ββ′ subunits. A relation between the decrease in number of transcription units and the observed higher rate of movement of DNA replication forks is discussed.

Feedback regulation of RNA polymerase subunit synthesis after the conditional overproduction of RNA polymerase in Escherichia coli

The beta and beta' subunits of RNA polymerase are thought to be controlled by a translational feedback mechanism regulated by the concentration of RNA polymerase holoenzyme. To study this regulation in vivo, an inducible RNA polymerase overproduction system was developed. This system utilizes plasmids from two incompatibility groups that carry RNA polymerase subunit genes under lac promoter/operator control. When the structural genes encoding the components of core RNA polymerase (alpha, beta and beta') or holoenzyme (alpha, beta, beta' and sigma 70) are present on the plasmids, induction of the lac promoter results in a two fold increase in the concentration of functional RNA polymerase. The induction of RNA polymerase overproduction is characterized by an initial large burst of beta beta' synthesis followed by a gradual decrease as the concentration of RNA polymerase increases. Overproduction of RNA polymerase in a strain carrying an electrophoretic mobility mutation in the rpoB gene results in the specific repression of beta beta' synthesis off the chromosome. These results indicate that RNA polymerase feedback regulation controls beta beta' synthesis in vivo.

Terminators of transcription with RNA polymerase from Escherichia coli: what they look like and how to find them

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.

Nucleotide sequence of the transcription unit containing the aroL and aroM genes from Escherichia coli K-12

The nucleotide sequence of 2,021 base pairs (bp) of DNA containing the Escherichia coli aroLM operon was determined, and the coding regions of both aroL and aroM were identified. The 501-bp intercistronic region between aroL and aroM contains an open reading frame which might encode a 63-residue protein. Northern blots with RNA from strains carrying multicopy aroL+ plasmids detected one longer (2,000-base) and two shorter (950- and 1,100-base) transcripts which contained aroL. It was concluded that the longest transcript, which was not abundant, spanned the entire operon and that the shorter transcripts resulted from either termination or posttranscriptional processing in the intercistronic region. The DNA upstream of aroL contains a number of imperfect palindromes which are closely homologous to known sites of regulation by the TyrR protein in other operons.

Attenuation and processing of RNA from the rpsO-pnp transcription unit of Escherichia coli

Ribosomal protein S15 and polynucleotide phosphorylase of E. coli are encoded by two adjacent genes, rpsO and pnp, respectively. Analysis of in vivo transcripts from these two genes shows that they are within the same operon (S15 operon). By correlating the 5' and 3' ends of their in vivo transcripts with the DNA sequence, we have identified several features of the operon structure. These features include a promotor upstream from rpsO, an attenuator downstream from rpsO and an RNA processing site between these two genes.

Transcription termination regions of coliphage T7 DNA: the effects of nusA1

We report the effects in vivo of four segments of coliphage T7 DNA upon expression, from an upstream promoter, of galK in plasmids of the pKO family. Three of the segments carry the known major or putative distal terminators of host-dependent T7 early transcription. The fourth carries a novel terminator and maps in the late region of T7. We report the efficiencies of termination in these regions: evidence, based on studies with the E. coli nusA1 mutation, for an involvement of the transcription factor NusA in events at the major early and novel terminators: and the nature of the latter transcription signal.

Nucleotide sequence of the alpha ribosomal protein operon of Escherichia coli

In Escherichia coli some 19 transcription units encoding the 52 ribosomal proteins are scattered throughout the genome. One of the units, the alpha operon, encodes genes for the ribosomal proteins S13, S11, S4 and L17 as well as the alpha subunit of RNA polymerase. We report here the complete 3.0 kb nucleotide sequence of the alpha operon. In addition, we have determined by S1 nuclease mapping the site of transcription termination in this operon.

Salmonella typhimurium rpoB and rpoC genes cloned on lambda phages

Salmonella typhimurium rpoB and rpoC genes, coding for the RNA polymerase subunits beta and beta', respectively, were isolated on lambda phages. Like their E. coli counterparts the two genes are closely linked and probably share a common promoter. The distribution of the target sites for several restriction enzymes, however, shows considerable divergence from the E. coli pattern.

Mutant of Escherichia coli with unusual patterns of rpoB,C expression in response to rifampicin and acridine orange

A mutation located near rpoB (89') in E. coli is responsible for unusual patterns of beta and beta ' (but not L7/L12) synthesis in response to the drugs rifampicin and acridine orange.

Evidence that pheV, a gene for tRNAPhe of E. coli is transcribed from tandem promoters

A DNA fragment of 487 bp containing a gene for tRNAPhe has been sequenced. Although the tRNAPhe sequence is identical to that of pheU (which maps at 94.5 min) the surrounding sequences are quite different. This sequence is thus that of a second gene for tRNAPhe (which we shall call pheV). In vitro transcription experiments and S1 mapping in vivo show the existence of two promoters separated by about 60 nucleotides. The second transcript starts only 3 nucleotides 5' from the tRNAPhe structural sequence. A DNA sequence characteristic of a rho-independent terminator is located 30 nucleotides 3' of the end of the structural gene and is shown to function efficiently in vitro.

Diphtheria toxin promoter function in Corynebacterium diphtheriae and Escherichia coli

The expression of the diphtheria tox228 gene encoding the nontoxic, serologically related CRM228 mutant diphtheria toxin has been analyzed in Corynebacterium diphtheriae and Escherichia coli. The diphtheria toxin promoter has been used to direct the expression of beta-galactosidase in E.coli, and the efficiency of promotion has been compared to that obtained with the lac promoter. Expression in C.diphtheriae is known to be dependent on the absence of iron, and we present for the first time direct evidence that this regulation occurs at the level of transcription. The 5' end of toxin mRNA maps at the same position in C.diphtheriae and E.coli, suggesting identical sequences to be recognized by C.diphtheriae and E.coli RNA polymerase. The diphtheria toxin promoter carries at position -34 a TTGATT sequence closely related to the E.coli -35 consensus sequence and in the -14 to -8 region a set of overlapping sequences with complete or partial homology to the E.coli -10 consensus sequence.

Consensus sequence for Escherichia coli heat shock gene promoters

We have identified promoters for the Escherichia coli heat shock operons dnaK and groE and the gene encoding heat shock protein C62.5. Transcription from each promoter is heat-inducible in vivo, and each is recognized in vitro by RNA polymerase containing sigma 32, the sigma factor encoded by rpoH (htpR) but not by RNA polymerase containing sigma 70. We compared the sequences of the heat shock promoters and propose a consensus promoter sequence, having T-N-t-C-N-C-c-C-T-T-G-A-A in the -35 region and C-C-C-C-A-T-t-T-a in the -10 region. These sequences differ from the consensus sequence recognized by holoenzyme containing sigma 70, the major sigma in E. coli. We suggest that the accumulated consensus sequences of promoters recognized by alternate forms of holoenzyme are compatible with a model in which sigma recognizes only the -10 region of the promoter.

An in vitro system to measure gene expression based on dipeptide synthesis

A simplified E. coli in vitro system has been developed to study gene expression based on the synthesis of the first di- or tripeptide of the gene product. Plasmids containing bacterial and chloroplast genes have been used as templates in this system. The expression of the E. coli L10 operon, which is under both transcriptional and translational control, has been investigated in some detail using the dipeptide system. A similar system has been developed, using eukaryotic translation components, to measure the expression of eukaryotic mRNA based on dipeptide formation.

Nucleotide sequence of the gene for Escherichia coli ribosomal protein S15 (rpsO)

The nucleotide sequence of the ribosomal protein gene rpsO (S15) and its flanking region were determined. The amino acid sequence of S15 protein deduced from the nucleotide sequence is in good agreement with the published amino acid sequence with one exception. The nucleotide sequence shows two probable promoter sites about 100 nucleotides upstream from the initiation codon (AUG) of rpsO. Inspection of the sequence also revealed structural homology between the distal part of rpsO and the reported S15 binding region in 16S rRNA.

Cloning with tandem gene systems for high level gene expression

A method has been devised for increasing the copy number of a gene (or genes) cloned into a plasmid while minimizing the size of the plasmid. If n copies of a transcriptional unit are cloned, including the promoter, coding region and terminator, the size of the plasmid will increase by n times the total size of the unit. However, if we borrow the concept of polycistronic operon and sandwich n structural genes, each with its own ribosome binding-site, between a promoter and a transcription terminator, there will be a space saving equivalent to n-1 promoters and n-1 transcription terminators. We have constructed plasmids in which an E. coli lipoprotein promoter is followed by 1 to 4 human leukocyte interferon genes and a transcription terminator. The applications of this method in genetic engineering are discussed.

The hisD-hisC gene border of the Salmonella typhimurium histidine operon

We have sequenced the hisD-hisC gene border of the Salmonella typhimurium histidine operon. The translation termination codon of the hisD gene overlaps with the translation initiation codon of the hisC gene in the manner AUGA. The Shine-Dalgarno sequence of the hisC gene is contained entirely within hisD and there is no intercistronic space since all of the bases are utilized in coding. Two mutations that alter the hisD-hisC gene border are analyzed. Both mutations simultaneously abolish the termination codon of hisD and modify the initiation codon of hisC. One of the mutations changes the hisC initiation codon from AUG to AUU. The AUU codon is 10 to 20% as efficient as AUG for initiation of translation of the hisC gene. The mutant hisC ribosome binding site is compared to the ribosome binding site of the Escherichia coli infC gene which has been reported to contain an AUU initiation codon. The role of overlapping termination/initiation codons in regulating translation of polycistronic mRNAs in bacterial operons is discussed.

Expression of the rpsO and pnp genes: structural analysis of a DNA fragment carrying their control regions

Precise physical mapping of the genes rpsO and pnp coding respectively for ribosomal protein S15 and polynucleotide phosphorylase together with regions involved in the regulation of their expression has been obtained by the analysis of in vitro deletion mutants. The results suggest that each gene has its own promotor, but that there is coexpression of rpsO and pnp. The nucleotide sequence of rpsO and of the beginning of pnp is presented and includes the presumed regulatory regions of these genes. Several features of the sequence support the mapping experiments and are discussed in relation to the expression of the ribosomal and pnp genes.

The internal regulated promoter of the deo operon of Escherichia coli K-12

Previous studies of the structure and regulation of the deo operon in Escherichia coli have localized an internal regulated promoter, called deoP3, in front of the two distal genes in the operon. We report here the nucleotide sequence of the distal portion of the deoA, the deoA-deoB intercistronic region and the first part of the deoB gene, and show that deoP3 overlaps the distal segment of the deoA gene. The location of the internal promoter and the transcriptional start site were determined by means of 1) sequence homology to the consensus promoter sequence of E. coli, 2) high resolution S1 nuclease mapping of in vivo transcripts and 3) in vivo regulation of beta-galactosidase from low as well as high copy number P31acZ protein fusion vectors.

The wild-type nucleotide sequence of the rpoBC-attenuator region of Escherichia coli DNA and its implications for the nature of the rifd18 mutation

To investigate the possibility that the unusual dominant rifampicin-resistance characteristic of the rifd18 allele of E. coli rpoB is due to a secondary, regulatory mutation, we have determined the nucleotide sequence of a 1.1 Kbp wild-type DNA fragment, including the transcriptional attenuator and translational start-site of rpoB. We have also re-investigated the previously published sequences of this region in lambda rifd18 and lambda rifd47 DNA. Our results indicate that all three sequences are identical, and reveal some errors in the published data. We discuss the basis of dominance of rifd18.

Evidence for antitermination in Escherichia coli RRNA transcription

The stable RNA operons of Escherichia coli do not exhibit polarity, even though they make an RNA product that is not translated. By contrast, most E. coli operons that specify proteins exhibit polarity if their translation is interrupted. The transcriptional component of this polarity depends on the action of Rho protein on the exposed mRNA, which results in premature transcription termination. Here we examine how a stable RNA operon (rrnG) transcript is protected from the Rho protein-mediated polarity response. We compared transcription from the ara and the rrnG promoters through a 16S DNA segment. In each case, the promoter-16S sequences were joined to a trp-lac fusion, and lacZ mRNA was examined in rho+ and rho-115 strains. We found significant Rho protein-dependent termination of transcripts from the ara promoter but little or no Rho protein effect on transcription from the rrnG promoter. We concluded that the transcript of the 16S ribosomal DNA segment does contain Rho protein-dependent transcription terminators, but there is an antitermination system in the rrnG control region that allows it to transcribe through those terminators.

Evidence for clustering of RNA polymerase and ribosomal protein genes in six species of Enterobacteria

32P-labelled DNA fragments from the E. coli beta operon were used as hybridisation probes for homologous DNA sequences in chromosomal digests of six species of Enterobacteria. In all species the hybridisation pattern suggested clustering of the genes comprising the beta operon.

A computer algorithm for testing potential prokaryotic terminators

The nucleotide sequences of 30 factor-independent terminators of transcription with RNA polymerase from E. coli have been compiled and analyzed. The standard features - a stretch of thymine residues and a preceding dyad symmetry - are shared by most sequences, but there are striking exceptions which indicate that these features alone are not sufficient to describe these sites. In two thirds of the sequences the 3'-half of the dyad symmetry contains the pentanucleotide CGGG (G/C) or a close derivative; about one third have TCTG or a close derivative just downstream of the termination point. The TCTG -box might be implied in termination of stringently controlled operons of E. coli. An algorithm to locate terminators in templates of known nucleotide sequence has been constructed on the basis of correlation to the distribution of dinucleotides along the aligned signal sequences. The algorithm has been tested on natural sequences of a total length of about 11,500 N. It finds all known independent terminators and only a few other sites, including some of the rho-dependent and putative terminators.

Relative activities of the transcriptional regulatory sites in the rplKAJLrpoBC gene cluster of Escherichia coli

The pattern of transcription of the rplKAJLrpoBC gene cluster of Escherichia coli appears to be complex. At least four different promoters and a transcriptional attenuator have been identified. To compare the relative effect of each of the putative promoters and the attenuator on transcription of these genes, we fused these regulatory sites to lacZ. These transcriptional fusions were constructed on lambda transducing phages so a single copy of each could be stably integrated into the chromosome. The level of beta-galactosidase in a lysogen of each phage reflects the activity of the transcriptional regulatory site. We find that the promoters preceding rplK (rplKp) and rplJ (rplJp) are indeed the major promoters of this gene cluster. The minor promoter before rplL (rplLp) is much weaker and contributes little to the transcription of the downstream genes. Under these conditions, we find no evidence of a promoter (rpoBp) in the rplL-rpoB intercistronic region. The attenuator (atn) terminates ca. 70% of the transcripts initiated at the promoters preceding it. Although we cannot rule out that some transcripts from rplKp may read through into rplJLrpoBC, we find that rplJp alone is sufficient for high-level expression of these genes.

Translational coupling of the trpB and trpA genes in the Escherichia coli tryptophan operon

We investigated whether there is translational coupling between the tryptophan operon trpB and trpA genes in Escherichia coli. A trp-lac fusion system was used in which part of the trpA gene is fused to the lacZ gene. This fusion protein has the translation initiation site of trpA but retains beta-galactosidase activity. We introduced a frameshift mutation early in trpB and measured its effect on transcription and translation of the trp-lac fusion. The mutation resulted in a 10-fold drop in beta-galactosidase activity but only a 2-fold drop in lacZ mRNA or galactoside transacetylase levels. An rho mutation restored the lacZ mRNA and transacetylase levels to those of the control but only increased the beta-galactosidase level to 20% that of the control. We conclude from these results that if the trpB gene is not translated, efficient translation of the trpA'-lac'Z mRNA does not occur and, thus, that these genes are translationally coupled. The implication of this finding for other studies with gene fusions is discussed.

Transcription analysis of the lexA gene of Escherichia coli: attenuation and cotranscription with the neighboring region

The lexA gene of Escherichia coli encodes a repressor of the genes whose expression is induced by the agents that result in DNA damage. In vivo transcripts of the lexA gene consisted of two species; mRNA-1 of 673 bases and mRNA-2 of approximately 3,000 bases. The transcription in vivo started at a site which was two-base pairs downstream from the in vitro initiation site reported previously. The majority of the transcription stopped at a series of T residues preceeded by a dyad symmetry located immediately after the lexA gene. A small fraction of the transcription passed through the termination site to form the mRNA of downstream gene(s) which would be related to the "SOS functions".

Nucleotide sequence of the promoter region of the E. coli lysC gene

The regulatory region of the lysC gene (that encodes the lysine-sensitive aspartokinase of Escherichia coli) has been identified and purified by the use of lysC-lacZ fusions. Its regulatory sequence has been determined. No signals similar to those described in the case of an attenuation mechanism could be found in the long leader sequence existing between the starts of transcription and of translation.

Bacteriophage P2 late promoters. Transcription initiation sites for two late mRNAs

Divergent transcription of two of the bacteriophage P2 late mRNAs, encoding genes QP and ONMLKRS, is initiated from opposite strands of the DNA in a region near the left end of the P2 genome. The first gene in each of these transcription units (P and O) has been located in the nucleotide sequence by amino-terminal sequence analysis of the P gene product and by DNA sequence determination of the single nucleotide changes in two O amber mutants. The 5' ends of the P and O gene mRNAs are separated by 109 nucleotide pairs in the DNA template. The locations of these 5' termini were determined by protection of end-labeled restriction fragments in RNA-DNA hybrids from digestion with nuclease S1. Sequence analysis of mRNA that had been labeled at the 5' end with [alpha-32P]GTP and guanylyl transferase confirmed that these termini resulted from initiation of transcription. The DNA sequences preceding the O and P transcription starts have poor homologies to the bacterial promoter consensus sequences at -10 and -35, consistent with the apparent requirement for phage-encoded proteins in the regulation of P2 late gene expression. The O and P promoter regions also have no detectable homology to each other in the -10 or -35 regions, and are unusually G + C-rich. There are, however, blocks of sequence homology within the transcribed region of each of these two late operons near the 5' end. Satellite phage P4 induces P2 late gene expression without the usual requirement for P2 DNA replication. The 5' ends of the P2 P and O gene transcripts are the same during P4 "transactivation" as during normal P2 late gene expression. Thus the regulation of P2 late gene expression by P4 does not involve a change in the site for initiation of transcription.

Complete nucleotide sequence of the E. coli glyA gene

The nucleotide sequence of the Escherichia coli glyA gene has been determined. The amino acid sequence predicted from the DNA sequence consists of 417 residues. After the coding region there is a 185 nucleotide sequence preceding the proposed transcription termination region for the glyA gene. This region is preceded by a G-C rich sequence that could form a stable stem-loop structure once transcribed, followed by an A-T rich sequence within which transcription appears to terminate. There is a long region of dyad symmetry and numerous smaller symmetrical regions between the site of translation termination and the proposed transcription termination region. These stem-loop structures show remarkable homology with intercistronic elements of other prokaryotic operons and may play a role in the regulation of glyA gene expression.

Synthesis of aspartate transcarbamoylase in Escherichia coli: transcriptional regulation of the pyrB-pyrI operon

The first committed reaction in pyrimidine biosynthesis in Escherichia coli and Salmonella typhimurium is catalyzed by the allosteric enzyme aspartate transcarbamoylase (aspartate carbamoyltransferase; carbamoylphosphate:L-aspartate carbamoyltransferase, EC 2.1.3.2), the product of the pyrB-pyrI operon. Regulation of the pyrimidine pathway is achieved in part by changes in the enzyme's catalytic activity as a function of the concentration of substrates and other metabolites as well as by variations in enzyme synthesis in response to changes in cellular levels of pyrimidine nucleotides. Although there is substantial evidence that UTP concentration has a marked influence on expression of the pyrB-pyrI operon, the mechanism of this control is not known. We have cloned the operon and determined the nucleotide sequence of the region preceding the first structural gene (pyrB). These studies show two regions sharing considerable homology with the consensus sequence of E. coli promoters, a segment that can code for a 44-amino-acid leader peptide, and a sequence very similar to that of the attenuator of the trp operon. RNA transcripts from several bacterial strains were studied by S1 nuclease mapping. Under conditions leading to extensive enzyme synthesis there was a large production of transcript whose 5' end correlated with the putative promoter closer to the structural genes. At low levels of operon expression there was little transcript in the extracts and both promoters appeared to serve as initiation sites. The results are interpreted in terms of transcriptional control of the pyrB-pyrI operon according to an attenuation model that differs in novel ways from the mechanisms proposed for the regulation of amino acid biosynthesis.