Cloning of the promoters of an Escherichia coli rRNA gene. New experimental system to study the regulation of rRNA transcription

A vast collection of microbial genes that are toxic to bacteria

In the process of clone-based genome sequencing, initial assemblies frequently contain cloning gaps that can be resolved using cloning-independent methods, but the reason for their occurrence is largely unknown. By analyzing 9,328,693 sequencing clones from 393 microbial genomes, we systematically mapped more than 15,000 genes residing in cloning gaps and experimentally showed that their expression products are toxic to the Escherichia coli host. A subset of these toxic sequences was further evaluated through a series of functional assays exploring the mechanisms of their toxicity. Among these genes, our assays revealed novel toxins and restriction enzymes, and new classes of small, non-coding toxic RNAs that reproducibly inhibit E. coli growth. Further analyses also revealed abundant, short, toxic DNA fragments that were predicted to suppress E. coli growth by interacting with the replication initiator DnaA. Our results show that cloning gaps, once considered the result of technical problems, actually serve as a rich source for the discovery of biotechnologically valuable functions, and suggest new modes of antimicrobial interventions.

An Escherichia coli gene in search of a function: phenotypic effects of the gene recently identified as murI

Earlier we reported that an open reading frame located at 89.5 min of the Escherichia coli map (ORFI) codes for a protein of unknown function that could be overexpressed and purified to homogeneity (G. Balikó, A. Raukas, I. Boros, and P. Venetianer, Mol. Gen. Genet. 211:326-331, 1988). In the work described here, we attempted to learn the function of this protein by inactivating the chromosomal gene and providing it or its deletion derivatives on temperature-sensitive plasmids. We found that the presence of the functional ORFI gene is essential; cells are not viable at the nonpermissive temperature or when the region coding for the C-terminal 50 amino acids of the protein is deleted. At intermediate temperatures or when the gene is overexpressed, characteristic changes occur in cell morphology, nucleoid separation during cell division, and supercoiling of plasmids. The possible mechanisms of these effects are discussed in view of the fact that Doublet et al. (P. Doublet, J. van Heijenoort, and D. Mengin-Lecreulx, J. Bacteriol. 174:5772-5779, 1992) recently identified the ORFI gene as murI, involved in D-glutamic acid biosynthesis.

The murI gene of Escherichia coli is an essential gene that encodes a glutamate racemase activity

The murI gene of Escherichia coli was recently identified on the basis of its ability to complement the only mutant requiring D-glutamic acid for growth that had been described to date: strain WM335 of E. coli B/r (P. Doublet, J. van Heijenoort, and D. Mengin-Lecreulx, J. Bacteriol. 174:5772-5779, 1992). We report experiments of insertional mutagenesis of the murI gene which demonstrate that this gene is essential for the biosynthesis of D-glutamic acid, one of the specific components of cell wall peptidoglycan. A special strategy was used for the construction of strains with a disrupted copy of murI, because of a limited capability of E. coli strains grown in rich medium to internalize D-glutamic acid. The murI gene product was overproduced and identified as a glutamate racemase activity. UDP-N-acetylmuramoyl-L-alanine (UDP-MurNAc-L-Ala), which is the nucleotide substrate of the D-glutamic-acid-adding enzyme (the murD gene product) catalyzing the subsequent step in the pathway for peptidoglycan synthesis, appears to be an effector of the racemase activity.

Identification of the Escherichia coli murI gene, which is required for the biosynthesis of D-glutamic acid, a specific component of bacterial peptidoglycan

The murI gene of Escherichia coli, whose inactivation results in the inability to form colonies in the absence of D-glutamic acid, was identified in the 90-min region of the chromosome. The complementation of an auxotrophic E. coli B/r strain by various DNA sources allowed us to clone a 2.5-kbp EcoRI chromosomal fragment carrying the murI gene into multicopy plasmids. The murI gene corresponds to a previously sequenced open reading frame, ORF1 (J. Brosius, T. J. Dull, D. D. Sleeter, and H. F. Noller. J. Bacteriol. 148:107-127, 1987), located between the btuB gene, encoding the vitamin B12 outer membrane receptor protein, and the rrnB operon, which contains the genes for 16S, 23S, and 5S rRNAs. The murI gene product is predicted to be a protein of 289 amino acids with a molecular weight of 31,500. Attempts to identify its enzymatic activity were unsuccessful. Cells altered in the murI gene accumulate UDP-N-acetylmuramyl-L-alanine to a high level when depleted of D-glutamic acid. Pools of precursors located downstream in the pathway are consequently depleted, and cell lysis finally occurs when the peptidoglycan content is 25% lower than that of normally growing cells.

Analysis of the complex transcription termination region of the Escherichia coli rrnB gene

The complex terminator region of the Escherichia coli rrnB gene was analyzed by subcloning the terminators T1 and T2 and the inverted repeats IR1 and IR2 individually, or in various combinations, in a normal or inverted orientation into a terminator probe vector. The in vivo terminating efficiency was assayed by measuring the galactokinase activity encoded by the downstream galK gene. Termination efficiencies of all fragments were compared in two constructs, differing in the presence or absence of readthrough translation over the investigated terminator signal. The following main conclusions were drawn. (a) T1 and T2 are both efficient terminators in isolated forms. (b) IR1 and IR2 have some terminating effect (much lower than the proper terminators), especially in the inverted orientation. Their presence modifies the effect of the proper terminators in a quite unpredictable way, especially if these regions are translated. (c) The terminators are not symmetrical; in the inverted orientation T1 is practically inactive and T2 termination is reduced. (d) Translation radically decreases the efficiency of the terminators. (e) Several sequences in the rrnB gene, upstream of the terminator region (one in the 16S RNA and one in the 5S RNA coding region), are very efficient in vivo terminators in the inverted orientation.

Saturation mutagenesis of an Escherichia coli rRNA promoter and initial characterization of promoter variants

Using oligonucleotide synthesis techniques, we generated Escherichia coli rrnB P1 (rrnB1p according to the nomenclature of B. J. Bachmann and K. B. Low [Microbiol. Rev. 44:1-56, 1980]) promoter fragments containing single base substitutions, insertions, deletions, and multiple mutations, covering the whole length of the promoter including the upstream activation sequence (UAS). The activities of 112 mutant promoters were assayed as operon fusions to lacZ in lambda lysogens. The activities of most mutants with changes in the core promoter recognition region (i.e., substitutions, insertions, or deletions in the region of the promoter spanning the -10 and -35 E. coli consensus hexamers) correlated with changes toward or away from the consensus in the hexamer sequences or in the spacing between them. However, changes at some positions in the core promoter region not normally associated with transcriptional activity in other systems also had significant effects on rrnB P1. Since rRNA promoter activity varies with cellular growth rate, changes in activity can be the result of changes in promoter strength or of alterations in the regulation of the promoter. The accompanying paper (R. R. Dickson, T. Gaal, H. A. deBoer, P. L. deHaseth, and R. L. Gourse, J. Bacteriol. 171:4862-4870, 1989) distinguishes between these two alternatives. Several mutations in the UAS resulted in two- to fivefold reductions in activity. However, two mutants with changes just upstream of the -35 hexamer in constructs containing the UAS had activities 20- to 100-fold lower than the wild-type level. This collection of mutant rRNA promoters should serve as an important resource in the characterization of the mechanisms responsible for upstream activation and growth rate-dependent regulation of rRNA transcription.

Visualization and quantitative analysis of complex formation between E. coli RNA polymerase and an rRNA promoter in vitro

We have established conditions that stabilize the interaction between RNA polymerase and the rrnB P1 promoter in vitro. The requirements for quantitative complex formation are unusual for E. coli promoters: (1) The inclusion of a competitor is required to allow visualization of a specific footprint. (2) Low salt concentrations are necessary since complex formation is salt sensitive. (3) The addition of the initiating nucleotides ATP and CTP, resulting in a low rate of dinucleotide production, is required in order to prevent dissociation of the complexes. The complex has been examined using DNAase I footprinting and filter binding assays. It is characterized by a region protected from DNAase I cleavage that extends slightly upstream of the region protected by RNA polymerase in most E. coli promoters. We find that only one mole of active RNA polymerase is required per mole of promoter DNA in order to detect filter-bound complexes. Under the conditions measured, the rate of association of RNA polymerase with rrnB P1 is as rapid as, or more rapid than, that reported for any other E. coli or bacteriophage promoter.

An Escherichia coli gene in search of a function

The rrnB gene of Escherichia coli is preceded by an open reading frame, which is cotranscribed with rrnB both in vivo and in vitro. It has earlier been shown that a 289 amino acid protein corresponding to this gene is actually synthesized in E. coli. In this paper we show that: (1.) The transcription of this gene diminishes the stringent response of the P1 promoter of the linked rrnB gene, but this is a cis effect and is not mediated by the protein product of the gene. (2.) The functional integrity of this gene seems to be essential, because efforts to replace it by a plasmid-coded copy mutagenized by Tn5 completely failed. (3.) The protein product of this gene was strongly overproduced by a recombinant plasmid, exploiting the principle of "translational coupling". This overproduction did not change the phenotype of the host cell significantly. The protein was purified to apparent electrophoretic homogeneity.

New regulatory features of the promoters of an Escherichia coli rRNA gene

Recombinant plasmids were constructed by fusing either promoter p1 or p2 or both promoters of the rrnB gene of Escherichia coli to a DNA fragment coding for the N-terminal alpha-peptide of beta-galactosidase. These plasmids contained various lengths of the 5'-leader region of rRNA as the 5'-terminal end of the alpha-peptide messenger. In some cases the entire 5'-terminal rRNA-coding sequence was removed, and alpha-peptide synthesis was governed by rac promoters formed by fusion of rrnBp2 and lac promoters. By measuring the level of alpha peptide, conclusions could be drawn about the activities of the promoters under various physiological conditions. It was found that the rate of transcription starting from promoter p1 or p2 might vary more than 10-fold during the growth cycle, showing a sharp maximum during outgrowth from the stationary phase into exponential growth or during nutritional shift-up. The target sequence of this regulation was localized to the leader region of the rrnB gene.

Expression vectors based on the rac fusion promoter

The -35 region of the rrnB P2 promoter and the -10 region of the lacZpo promoter-operator were fused to form the strong and regulatable rac promoter. Vectors were constructed that allow the attachment of protein-coding sequences to the beta-galactosidase alpha-peptide (LacZ alpha) in any reading frame. By introducing a high-copy-number mutation, the synthesis of a LacZ alpha-chloramphenicol acetyltransferase fusion protein reached more than 60% of total cell protein in Escherichia coli.

A novel type of bacterial transcription unit, specifying mRNA, rRNA, and tRNA

Previously it had been shown that a chromosomal region preceding the rrnB gene of Escherichia coli contains an 867 base pair-long open reading frame and it is co-transcribed with the rrnB gene both in vitro and in vivo. Here we report that minicells programmed by recombinant plasmids carrying this region or a deletion derivative of it, synthetise a protein of the expected size. Thus this transcription unit codes for mRNA, rRNA, and tRNA.