Characterization of promoter-cloning plasmids: analysis of operon structure in the rif region of Escherichia coli and isolation of an enhanced internal promoter mutant

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

Mapping of sequences required for the translation of the beta subunit of Escherichia coli RNA polymerase

Previous experiments using expression plasmids which overproduce the beta and beta' subunits of Escherichia coli RNA polymerase suggested that regions considerably upstream of the start of the rpoB gene, which encodes the beta subunit, are required for its efficient synthesis. To further delineate the required regions, a collection of genetic constructs that contained varying amounts of the region either upstream or downstream of the translational start of rpoB was assembled. Measurements of beta and beta' synthesis and rpoB mRNA production from a series of rpoBC expression plasmids indicated that sequences extending more than 43 bp but less than 79 bp upstream of rpoB are required for the efficient translation of rpoB mRNA. This result was confirmed by beta-galactosidase measurements from a series of rpoB-lacZ fusions that have the same set of end points upstream of rpoB as the expression plasmids. A second set of gene fusions containing differing amounts of the sequence distal to the start of rpoB fused in frame to lacZ revealed that more than 29 bp but less than 70 bp of rpoB was required for efficient translation.

Effect of Escherichia coli nusG function on lambda N-mediated transcription antitermination

The Escherichia coli Nus factors act in conjunction with the bacteriophage lambda N protein to suppress transcription termination on the lambda chromosome. NusA binds both N and RNA polymerase and may also interact with other Nus factors. To search for additional components of the N antitermination system, we isolated host revertants that restored N activity in nusA1 mutants. One revertant, nusG4, was mapped to the rif region of the E. coli chromosome and shown to represent a point mutation near the 3' end of the nusG gene. The nusG4 mutation also suppressed nusE71 but not nusASal, nusB5, nusC60 (rpoB60), or nusD026 (rho026). However, nusG+ expressed from a multicopy plasmid suppressed nusD026 and related rho mutants for both lambda and phage T4 growth. These results suggest that NusG may act as a component of the N antitermination complex. In addition, the data imply a role for NusG in Rho-dependent termination.

A novel RNA product of the tyrT operon of Escherichia coli

The tyrT operon of E. coli and several other tRNA operons of E. coli show striking structural features: they contain repeated sequence units including a 19bp motif resembling the 3' end of the corresponding mature tRNA. A novel RNA, encoded by the repeated sequence of the tyrT operon, was identified. The RNA, characterized by primer extension and Nuclease-S1 analysis, contained 171 nucleotides and terminated with the 19bp motif of the CCA-end of tRNA(1Tyr). The RNA, designated as rtT RNA, is probably released from the primary transcript of tyrT during tRNA processing, it includes the coding capacity for the arginine rich peptide Tpr. Predictions of secondary folding resulted a rather stable RNA structure with a free energy of -44.3kcal/mol. A weak ribosome binding site was found, preceding the second possible AUG initiator codon for Tpr. The comparison of rtT RNA with putative transcripts from the repeated sequences associated with related tRNA genes showed common features with respect to primary structure, arrangement and secondary folding. In E. coli cultures the lag-phase during growth, caused by transient glycine or by isoleucine limitation, was found to be overcome or markedly shortened in the presence of rtT RNA. These and previously reported results suggest a modulatory effect of rtT RNA on stringent response.

In vivo analysis of overlapping transcription units in the rplKAJLrpoBC ribosomal protein-RNA polymerase gene cluster of Escherichia coli

Transcription of the rplKAJLrpoBC ribosomal protein (rpl) RNA polymerase (rpo) gene cluster is governed by a complex set of signals. To dissect the transcription units active in vivo and to quantify the relative contribution of each, an extensive array of rplKAJLrpoB/lacZ gene fusions were constructed on lambda phage derivatives and introduced in single copy into the chromosomes of lac- cells. Measurements of beta-galactosidase production from fusions containing wild-type and/or mutagenized rplrpo DNA fragments permitted the establishment of high-resolution transcription profiles of the gene cluster. The results show that transcription initiated at the upstream rplKp promoter (located just before rplK) does not terminate before the rplJp promoter (located upstream from rplJ), but instead reads through into the distal genes. In addition, rplJp continues to function efficiently in the presence of readthrough transcription from rplKp. As a result the rplJL genes are transcribed at almost twice the frequency of the upstream rplKA genes. However, the transcription of rpoB, which is situated downstream from the previously identified attenuator (rpoBa), is only marginally increased (20%) when both promoters are present. This suggests that although both transcription units overlap, transcriptional termination at rpoBa is modulated in response to the frequency of initiation from both promoters.

FIS-dependent trans-activation of tRNA and rRNA operons of Escherichia coli

Two mechanisms controlling stable RNA synthesis have been described: growth rate-dependent control and stringent response. Although the mechanism underlying growth rate-dependent control is still a matter of dispute, this control is commonly assumed to operate through repression of transcription initiation of stable RNA operons. The same is true for the stringent response. Here we show that the cell utilizes an additional control system operating through activation of the thrU(tufB) operon. This operon, the tyrT and the rrnB operon share a common trans-activating protein that binds to cis-acting DNA regions upstream of the promoters of the two tRNA operons and of the P1 promoter of the rrnB operon. Conceivably, more stable RNA operons may be regulated by trans-activation. Both in vivo and in vitro experiments show that the Escherichia coli protein FIS (Factor for Inversion Stimulation) is involved in the trans-activation. This protein is known to stimulate the inversion of various DNA segments by binding to cis-acting recombinational enhancers and functions as a host factor for the bacteriophages Mu and Lambda.

The secE gene encodes an integral membrane protein required for protein export in Escherichia coli

Genetic screening and selection procedures employing a secA-lacZ fusion strain repeatedly have yielded mutations in four genes affecting the protein export pathway of Escherichia coli. These genes are secA, secD, prlA/secY, and secE. We discuss the significance of the failure to find new sec genes after extensive use of this approach. One of the genes, secE, has been characterized in some detail. From the DNA sequence of the gene and analysis of alkaline phosphatase fusions to the SecE protein, we propose that it is a 13,600-dalton integral cytoplasmic membrane protein. The data presented here and in the accompanying paper strongly suggest that secE has an important role in E. coli protein export.

Expression of cloned rpoB gene of Escherichia coli: a genetic system for the isolation of dominant negative mutations and overproduction of defective beta subunit of RNA polymerase

The rifampin resistance rifD18 allele of rpoB, carried on the expression plasmid pXT7 beta, is controlled by a strong bacteriophage T7 late promoter and two weak Escherichia coli promoters. Depending on the host strain, pXT7 beta specifies different levels of Rifr beta subunit, providing a system for the isolation, maintenance, and overexpression of dominant lethal alleles of rpoB. In rpoB+ hosts, pXT7 beta confers the Rifr phenotype on the Rifs host. Negative rpoB mutations in the plasmid DNA can thus be scored by screening transformants for Rifs. In an rpoB(Am) supD(Ts) host in which chromosomal rpoB expression is decreased as the temperature goes up, some of the negative plasmid-borne rpoB mutations displayed a dominant phenotype. In a host harboring inducible T7 RNA polymerase, the defective beta subunits could be overexpressed independently of the E. coli transcriptional machinery. With this system, we isolated several negative rpoB mutations induced in vitro by hydroxylamine. Seven of the mutant rpoB alleles, when overexpressed, were found to specify normal-size beta polypeptides. Two of them displayed the dominant lethal phenotype in the rpoB(Am) supD(Ts) background. We also constructed a mutation (rpoB1800) in which 24 carboxy-terminal amino acids were substituted with a random 19-amino-acid sequence. The nonfunctional rpoB1800 beta polypeptide was isolated and assembled in vitro into the core enzyme molecule.

The nucleotide sequence of the Escherichia coli rts gene

The nucleotide sequence of rts, an essential Escherichia coli gene, has been determined. Transformation of an rts mutant with the plasmid, pJAF1, containing the rts gene resulted in rescue of the defect. The transformation experiments indicate that the rts gene is distinct from the flanking birA, tRNA and tufB genes.

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.

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.

Growth rate-dependent regulation of RNA polymerase synthesis in Escherichia coli

The rate of synthesis of the beta and beta' subunits of RNA polymerase relative to the rate of synthesis of total protein was found to remain constant with increasing steady state growth rate. This is in contrast to the relative synthesis rates of ribosomal proteins which are known to increase with growth rate. Yet the ratio of the rate of transcription of the ribosomal protein (rplJL) and RNA polymerase (rpoBC) domains of the rplKAJLrpoBC gene cluster was found to be invariant. Fusions to lacZ were used to relate the rate of transcription of the rplKAJL genes to the rate of synthesis of total protein. No change was seen at growth rates above 0.8 doublings per hour. This indicates that the growth rate-dependent expression of these ribosomal proteins is regulated at the post-transcriptional level. However because both the relative rate of transcription of rpoBC and rate of synthesis of beta and beta' were found to remain invariant over this growth range it suggests the expression of these RNA polymerase subunits is regulated at the transcriptional level.

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.

Transcriptional analysis of the leading region in F plasmid DNA transfer

Transcriptional activity associated with the leading region (53.8-66.7F) in F DNA transfer has been shown by RNA-DNA hybridization studies to occur on the anterior segment extending from 59.4 to 66.7F. Promoter-probe analysis of cloned leading region segments detected two promoters within the transcribed portion of the leading region. The promoter active across the 64.7F EcoRI site on the transferred F strand was associated with the expression of two polypeptides, 6d and 13.5p, located between 64.7-66.6F. However, no definite role could be ascribed to the second promoter operative through the 66.6F Bg/II site located in close proximity to oriT, the origin of transfer.

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.

Transcription of a gene cluster coding for two aminoacyl-tRNA synthetases and an initiation factor in Escherichia coli

The alpha and beta subunits of phenylalanyl-tRNA synthetase are encoded by the pheS and pheT genes, respectively. These genes are clustered closely together with the genes for threonyl-tRNA synthetase (thrS) and translation initiation factor IF3 (infC); the gene order is thrS infC pheS pheT. We have used two methods to study the transcription pattern within this cluster. The first was the in vitro transcription of DNA restriction fragments with purified RNA polymerase, followed by fractionation of the RNA products by polyacrylamide gel electrophoresis. The second method was the mapping of promoters by means of the "abortive initiation" reaction of McClure and co-workers. This procedure consists of the incubation of RNA polymerase with DNA restriction fragments plus one nucleoside monophosphate and one [alpha-32P]nucleoside triphosphate; the polymerase synthesizes dinucleotide products of known sequence at promoter sites in the DNA. We found that transcription initiated at an internal site within infC (designated P1), and at two promoter sites between infC and pheS (designated P2 and P3). Transcription terminated at two sites about 200 nucleotides apart, located just before pheS. The initiation and termination signals were arranged so as to yield a nested set of overlapping transcripts. At the P1 promoter, transcription initiated with G-C, at P2 with A-C and sometimes A-G, and at P3 with G-U. Promoter activity was also found in a 3000-base interval that includes the start of the thrS gene; eight or nine transcripts (not mapped in detail) were observed, which started with at least four different dinucleotides. All major initiation sites in the gene cluster represented purine starts, although some pyrimidine initiation was observed in trace amounts. No promoter activity was found between pheS and pheT with either of the two techniques; this observation supports the conclusion that these genes are co-transcribed. No evidence was found for any promoter between the termination sites and the beginning of the pheS gene. It is suggested that one of the terminators is an attenuation site controlling the extension of transcription into pheS and pheT. Attenuation may explain the observed regulation of phenylalanyl-tRNA synthetase by the amino acid supply.

Computer methods to locate signals in nucleic acid sequences

This paper describes computer methods for locating signals in nucleic acid sequences. The signals include ribosome binding sites, promoter sequences and splice junctions. The methods are of use both to those trying to interpret the function of newly determined sequences and to those studying the molecular mechanisms involved in the recognition of these special signal sequences.

Compilation and analysis of Escherichia coli promoter DNA sequences

The DNA sequence of 168 promoter regions (-50 to +10) for Escherichia coli RNA polymerase were compiled. The complete listing was divided into two groups depending upon whether or not the promoter had been defined by genetic (promoter mutations) or biochemical (5' end determination) criteria. A consensus promoter sequence based on homologies among 112 well-defined promoters was determined that was in substantial agreement with previous compilations. In addition, we have tabulated 98 promoter mutations. Nearly all of the altered base pairs in the mutants conform to the following general rule: down-mutations decrease homology and up-mutations increase homology to the consensus sequence.

The lethal effect of a plasmid resulting from transcriptional readthrough of rplJ from the rplKA operon in Escherichia coli

A high-copy plasmid, pGA217, which carries a deletion (lacking the carboxy-terminal 20 amino acids) of the structural gene for ribosomal protein L10 (rplJ) is lethal to the cell in the absence of the gene (rplL) for r-proteins L7/L12, but only if the upstream operon for r-proteins L11 (rplK) and L1 (rplA) is present on the same plasmid. Measurements of beta-galactosidase activity of a hybrid protein expressed by a rplL-lacZ fusion indicated that the L10 fragment peptide which lacks the carboxy-terminal 20 amino acids is capable of exerting feedback regulation. Double transformation experiments with two compatible plasmids showed that the detrimental effect of the rplJ deletion on pGA217 can be reversed by the addition of a second plasmid which carries a functional gene for L7/L12. These two pieces of evidence suggest that the lethal effect of pGA217 is due to its property of feeding back on L7/L12 production from the chromosomal rplK gene. The upstream rplKA operon was inferred to have a cis-acting, stimulating effect on rplJ expression from the following evidence: (1) donor plasmids carrying the genes for L11 and/or L1 fail to exert a trans-acting effect, (2) deletion mutants which removed portions of rplK and/or rplA, but maintained the rplKA promoter, rplKp, still retained a severe growth-inhibiting effect. We suggest that these results can be explained by assuming that there is transcription from the rplKA promoter through rplJ and perhaps beyond.

Insertions of transposon Tn5 into ribosomal protein PNA polymerase operons

The genetic organization and interrelationships between the two ribosomal protein transcription units (the L11 and L10 operons) from near 89 min on the Escherichia coli chromosome were studied by using insertional mutations generated by the kanamycin-resistant transposable element Tn5. The polar effects of Tn5 insertions on the expression of the L11, L1, L10, and L12 ribosomal protein genes and the beta RNA polymerase subunit gene were examined (i) by the level of beta-galactosidase activity generated from L10-lacZ and beta-lacZ gene fusions, (ii) by direct sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the proteins specified by plasmid ribosomal protein genes in UV-irradiated maxicells, and (iii) by urea-polyacrylamide gel electrophoresis of plasmid- and chromosome-specified L12 protein. The results confirmed the organization of these genes into two transcription units as follows: PL11, rplK (L11), rplA (L1), PL10, rplJ (L10), rplL (L12), rpoB (beta). . .; they also localized the position of the PL10 promoter within an 80-nucleotide region near the end of the L1 gene. The results also support the idea that the translational regulatory proteins for the L11 and L10 operons are L1 and L10, respectively, and that the expression of the L12 gene is closely linked to L10 gene expression.

Genetic analysis of two bacterial RNA polymerase mutants that inhibit the growth of bacteriophage T7

The Escherichia coli mutants 7009 and BR3 are defective in the growth of bacteriophage T7. We have previously shown that both of these mutant hosts produce an altered RNA polymerase which is resistant to inhibition by the T7 gene 2 protein (De Wyngaert and Hinkle 1979). In both strains, the mutation which prevents T7 growth is closely linked to rifA (rpoB). Both mutants are complemented by transformation with a multicopy plasmid carrying rpoB and rpoC but not by a plasmid carrying only rpoB. This indicates that the mutations reside in rpoC, the structural gene for the beta' subunit of RNA polymerase. When a single copy of the wildtype rpoC allele is introduced into the mutant using the transducing phage lambda drifd18, the mutant allele is dominant over wildtype. The lambda drifd18 transductant also remains unable to support the growth of T7 in the presence of rifampin. This supports our conclusion that the mutation is in rpoC. We have measured the growth of T7 phage, the kinetics of phage DNA synthesis, and the structure of replicative DNA intermediates in several transductants, and compared these results with those obtained in the original mutant strains.

Construction and characterization of E. coli promoter-probe plasmid vectors. III. pBR322 derivatives with deletions in the tetracycline resistance promoter region

Deletions of the promoter region for the tetracycline-resistance (Tcr) gene(s) of pBR322 were constructed in order to generate new promoter-probe plasmid cloning vectors. The deletions were constructed in vitro by exonuclease digestion at the HindIII site and blunt-end ligation of the digestion products. Plasmids which lost the HindIII site but retained the EcoRI site carried deletions ranging from 5 to 60 bp. Some of the plasmids lacked the nucleotide sequences required for initiation of transcription from the Tcr promoter and "anti-Tcr" promoter. Three of the promoter-deletion plasmids (containing deletions of 5-29 bp) formed tight-binding complexes with RNA polymerase in vitro, despite their tetracycline sensitive phenotype. One deletion plasmid, pPV33, retained three out-of-phase stop codons located between the promoter-cloning site (EcoRI) and the translational start codon for the tetracycline resistance gene. These features give pPV33 several advantages over previously described promoter-cloning vehicles.

Effect of rifampicin on expression of lacZ fused to promoters or terminators of the E.coli rpoBC operon

The genes encoding the beta and beta' subunits of RNA polymerase in E.coli lie downstream of at least two ribosomal protein genes in a single unit of transcription. Treatment of E.coli with rifampicin, under conditions producing partial inhibition of general RNA synthesis, can strongly stimulate transcription of the polymerase genes, while activating the neighbouring ribosomal genes only slightly. We have investigated the mechanism of this effect by fusing strong promoters, a weak internal promoter, and an attenuator of the polymerase operon to the lacZ gene, in derivatives of plasmid pMC81. Studies of these fusions confirm our conclusion, based on similar fusions to galK, that rifampicin can foster readthrough of transcriptional terminators. They also suggest the existence of extra terminators and anti-termination elements in the above transcription unit.

Evidence that rifampicin can stimulate readthrough of transcriptional terminators in Escherichia coli, including the attenuator of the rpoBC operon

The genes encoding the beta and beta' subunits of RNA polymerase in E.coli, rpoB and rpoC, lie downstream of at least two ribosomal protein genes, rplJ (encoding L10) and rplL (L7/12), in a common operon. All four genes are served by promoter PL10, and an attenuator (partial terminator) of transcription, t1, lies between rplJL and rpoBC. Treatment of E.coli with rifampicin, under conditions producing partial inhibition of general RNA synthesis, can stimulate transcription of rpoBC. We have investigated the locus of this effect by fusing PL10 and t1 separately to galK, in suitable plasmids. Our studies of these fusions, and similar fusions involving transcriptional terminators derived from coliphage T7, indicate that low concentrations of rifampicin cause increased readthrough of several different transcriptional terminators in E.coli in vivo, including rpo t1. We discuss whether or not this unspecific mechanism is solely responsible for the observed stimulatory effects of the drug on rpoBC transcription.

The primary structure of E. coli RNA polymerase, Nucleotide sequence of the rpoC gene and amino acid sequence of the beta'-subunit

The primary structure of the E. coli rpoC gene (5321 base pairs) coding the beta'-subunit of RNA polymerase as well as its adjacent segment have been determined. The structure analysis of the peptides obtained by cleavage of the protein with cyanogen bromide and trypsin has confirmed the amino acid sequence of the beta'-subunit deduced from the nucleotide sequence analysis. The beta'-subunit of E. coli RNA polymerase contains 1407 amino acid residues. Its translation is initiated by codon GUG and terminated by codon TAA. It has been detected that the sequence following the terminating codon is strikingly homologous to known sequences of rho-independent terminators.

Evidence for an internal promoter preceding tufA in the str operon of Escherichia coli

We constructed plasmids carrying tufA from which the major promoter for the rpsL-rpsG-fus-tufA operon (also called the str operon) had been removed. These plasmids continued to express tufA, as judged by the ability to complement mocimycin resistance and by electrophoretic analysis of synthesized proteins. Tn5 transpositions into fus, the gene for elongation factor G, which lies immediately on the 5' side of tufA, failed to obstruct the expression of tufA. The subcloning of a 2,000-base-pair PstI-SmaI DNA fragment (containing the intercistronic region between tufA and fus, the distal portion of fus, and the proximal portion of tufA) next to promoterless tetracycline resistance genes (tet) yielded a plasmid that was capable of bestowing resistance to 12 microgram of tetracycline per ml. The removal of an EcoRI fragment that lies within fus destroyed the ability of the 2,000-base-pair PstI-SmaI fragment to promote the transcription of tet. These data indicate that, in addition to the operon's major promoter rpsLp, there is an internal promoter, tufAp, which can be used for the transcription of tufA, tufAp probably lies within fus, about 50 base pairs upstream from its 3' end and 120 base pairs from the start codon of tufA. The relative activities of tufB and of tufA-from-tufAp were estimated by a comparison of beta-galactosidase activities of almost identical EF-Tu-beta-galactosidase protein fusions; they were approximately equal.

Internal promoters of the rpoBC operon of Escherichia coli

Four ribosomal protein genes, rplA, rplJ, rplK and rplL form an operon in E. coli together with the genes rpoB and rpoC which encode the beta and beta' subunits of RNA polymerase. Transcription is initiated principally at two promoters, PL11 and Pl, the overall structure of the operon being (in the direction of transcription) PL11 rplK rplA Pl rplJ rplL rpoB rpoC. Here we describe studies of phage lambda derivatives carrying various segments of this operon, which demonstrate the existence of at least three additional weak internal promoters, and help to define their positions and strengths.

Cloning and the nucleotide sequence of the genes for Escherichia coli ribosomal proteins L28 (rpmB) and L33 (rpmG)

The specialized transducing bacteriophage lambda dpyrE DNA was used as a source of DNA to clone two ribosomal protein genes rpmB (L28) and rpmG (L33) on the cloning vehicle pACYC184. Using one of these plasmids, the nucleotide sequence of these two genes and their flanking regions were determined. The amino acid sequences of both proteins deduced from the nucleotide sequences match with the amino acid sequences previously determined, with one exception. The nucleotide sequences suggest that these two ribosomal protein genes are cotranstribed. There was no expression of the second gene of the operon, rpmG, in the absence of the 5' sequences adjacent to the first gene, rpmB. Observation of the structure of mRNA also strongly supports the idea that rpmB and rpmG are in a single transcription unit whose order is: rpmBp-rpmB-rpmG-rpmGt.

Organization and nucleotide sequence of a new ribosomal operon in Escherichia coli containing the genes for ribosomal protein S2 and elongation factor Ts

We report the nucleotide sequence of the four min region of the Escherichia coli genetic map that includes the genes for ribosomal protein S2 (rpsB) and translation elongation factor EF-Ts (tsf), and the possible location of regulatory sites within this two gene operon. The data indicate that the gene order is: rpsBp-rpsB-tsf-tsft. One potential regulatory site is a 16 nucleotide sequence in the rpsB leader region encompassing the ribosome binding site and the translation initiation codon. This has a high degree of homology with nucleotides 8 through 23 on the 5' end of 165 ribosomal RNA, and might signify a sequence that is necessary for post-transcriptional control of rpsB expression. The data allow one to infer the amino acid sequences of S2 and EF-Ts.

Location of the tufB promoter of E. coli: cotranscription of tufB with four transfer RNA genes

Previous nucleotide sequence studies have demonstrated that the structural genes for four transfer RNA species (thrU, tyrU, glyT and thrT) are positioned close to one another and near tufB, one of the structural genes for elongation factor Tu. We have carried out experiments to determine the position of the tufB promoter and thus to infer whether these five genes are in a single transcription unit. tufB cloned on plasmids was fused to Tc (in operon fusion) or to lacZ (in gene fusion). These plasmids were then subjected to in vitro deletion to locate the promoter responsible for tufB transcription. In addition, the ability of wild-type tufB to complement kirromycin resistance was determined with deletion plasmids. The results indicate that the major promoter for tufB lies upstream from the four transfer RNA genes, and that there might be at least one weak internal promotor, possibly adjacent to tufB. Assuming that the four tRNA genes that lie between the major promoter and tufB are also transcribed from that promoter, we suggest that all five genes lie in a single transcription unit (thrUp-thrU-tyrU-glyT-thrT-tufB-tufBt) whose primary transcript is thus both a transfer RNA precursor and messenger RNA.

Regulation of the synthesis of E. coli elongation factor Tu

Rapidly growing E. coli with two active genes (tufA, tufB) for elongation factor (EF) Tu contains three times as much EF-Tu (tuf) mRNA as EF-G (fus) mRNA on a molar basis, but about seven times as much EF-Tu as EF-G or ribosomes. The concentration and translational efficiency of fus (EF-G) mRNA is about that for ribosomal protein mRNAs. The high molar concentration of EF-Tu relative to EF-G or ribosomes is achieved in part by translating tuf mRNA more efficiently than these other mRNAs. In a tufA+ tufB-: : Mu strain, the tuf:fus mRNA ratio is 1, but the concentration of EF-Tu and tuf mRNA is the same as in the wild-type strain. Thus cells with only an active tufA gene increase the concentration but not the translational efficiency of tuf mRNA. In such cells the concentration of fus mRNA is almost three times that in the wild-type strain. Because the tufA gene is distal to but cotranscribed with the fus gene as part of the four gene str operon, the wild-type concentration of tuf mRNA in these tufB- cells must be produced by increasing the concentration of transcript corresponding to the entire str operon. Thus transcription of the tufA gene can only proceed from the str promoter. Extracts of the tufB- cells contain tuf transcripts that correspond not only in size to the entire 4.5 kb str operon, but also to the size (approximately 1 kb) of a tuf gene. Our evidence suggests that this 1 kb tuf transcript is derived by posttranscriptional modification of the primary str operon transcript and that this modification could in part explain the high translational efficiency of tuf mRNA.