Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli

Evidence that a nucleotide sequence, "boxA," is involved in the action of the NusA protein

We report the isolation of a mutation, boxA1, in the nutR region of the phage lambda genome. The nutR region, located downstream of the pR promoter, includes the site nutR where the lambda N protein is thought to act to render subsequent transcription termination-resistant. We have previously suggested that the boxA sequence, 5'CGCTCTTA3' (or its RNA analog), located 8 bp promoter-proximal to nutR, might be the recognition site for the E. coli host factor, NusA, which has been shown to be necessary for N action. The boxA1 mutation, an A:T to T:A transversion, results in a changed boxA sequence upstream of nutR, CGCTCTTT. This change is necessary for lambda to effectively use the NusA of Salmonella typhimurium, a NusA function not normally active with the N product of lambda. Other lambdoid phages with unique N functions and nut sites that are normally active with the NusA of Salmonella have boxA sequences with the terminal three Ts. Moreover, sequences closely resembling boxA have been found near transcription termination sequences in E. coli operons where NusA has been shown to be involved in termination. These findings identify boxA as an important recognition signal for the NusA protein.

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.

The complete nucleotide sequence of a 16S ribosomal RNA gene from a blue-green alga, Anacystis nidulans

The complete nucleotide sequence of a 16S ribosomal RNA gene from a blue-green alga, Anacystis nidulans, has been determined. Its coding region is estimated to be 1,487 base pairs long, which is nearly identical to those reported for chloroplast 16S rRNA genes and is about 4% shorter than that of the Escherichia coli gene. The 16S rRNA sequence of A. nidulans has 83% homology with that of tobacco chloroplast and 74% homology with that of E. coli. Possible stem and loop structures of A. nidulans 16S rRNA sequences resemble more closely those of chloroplast 16S rRNAs than those of E. coli 16S rRNA. These observations support the endosymbiotic theory of chloroplast origin.

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

The promoters of the rrnB gene of Escherichia coli have been cloned on a multicopy, pBR322-derived plasmid by deleting most of the structural part of rrnB and fusing the terminators of the gene immediately to the promoters. Several further deletions were constructed to vary the promoter-terminator distance, destroy or damage selectively any of the promoters or terminators, and vary the distance between the two pairs of P1 P2 and P3 P4 promoters. All these transcription signals were shown to function on the plasmids in vitro and in vivo. The truncated in vivo transcription products initiated at the P1 and P2 promoters of the recombinant plasmids were found to be stable, and the accumulated transcripts could be easily distinguished from the chromosome-coded rRNA. This provides a convenient experimental system to study the regulation of rRNA biosynthesis.

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.

Regions of DNA involved in the stringent control of plasmid-encoded rRNA in vivo

We have examined the transcription of two plasmid-encoded, stable RNAs; a shortened 16S ribosomal RNA and the spacer transfer RNA2Glu from the Escherichia coli rrnB operon. Plasmid deletions were constructed in vitro, in order to examine the DNA regions required for stringent control of rRNA expression in vivo during amino acid starvation. We find that rRNA synthesized from plasmids does exhibit a relA-dependent, stringent response. The DNA sequences required for this regulation do not extend beyond 20 bases downstream of the P1 transcription initiation site. Deletion of P2, the second of the two tandem rRNA promoters, does not weaken the stringent control of transcripts from P1. These results demonstrate that pause sites for RNA polymerase identified in vitro do not play a significant role in the stringent control of rRNA synthesis in vivo and imply that stringent regulation takes place at the level of initiation, rather than elongation, of transcription. Surprisingly, we find that the presence of extra intact rrnB operons (carried by a multicopy plasmid) reduces the magnitude of the stringent response.

Differential stringent control of the tandem E. coli ribosomal RNA promoters from the rrnA operon expressed in vivo in multicopy plasmids

The tandem P1, P2 promoter region of the rrnA ribosomal operon has been fused to the t1, t2 terminator region of the rrnB operon in pBR322 plasmid derivatives. This deletes most internal RNA structural elements ordinarily processed out of ribosomal operon transcripts. In vivo as well as in vitro transcripts arising from both promoters terminate predominantly in the t1 terminator region about 40 base pairs beyond the mature rrnB 5S RNA gene. Stringent control of the P1 and P2 promoted transcripts has been assessed in vivo. In these plasmid fusions, the upstream (P1) promoter activity was subject to stringent control, while the downstream (P2) promoter activity was inhibited by amino acid starvation in both stringent and relaxed hosts. A plasmid with an additional deletion of the P2 region also showed stringent regulation of the P1 promoter.

Identification of two new promoters probably involved in the transcription of a ribosomal RNA gene of Escherichia coli

The DNA sequence in the region preceding the rrnB gene of Escherichia coli was determined up to the 1821st nucleotide upstream from the beginning of the sequence coding for mature 16 S rRNA. In vitro transcription experiments indicated the presence of two new promoters in this region, located more than 1 kb upstream from the known P1 and P2 promoters of rrnB. Previous electron microscopic studies demonstrated that these sites bind RNA-polymerase very strongly. In vitro transcription, starting at these sites reads through the entire region into the rrnB gene without termination. A similar uninterrupted transcription into rrnB in vivo can be demonstrated by S1-mapping, and by fusing the DNA containing the new promoters (but not P1 and P2) to the lacZ gene. Thus it seems likely that these promoters (P3 and P4) belong functionally to the rrnB gene and play some role in its regulation of expression.

Functional interrelationship between two tandem E. coli ribosomal RNA promoters

The Escherichia coli chromosome carries seven cistrons encoding ribosomal RNA sequences. In all cases studied, in vitro and in vivo, it has been established that transcription is initiated from two tandem promoters. The expression of the rRNA cistrons is regulated in response to growth rate as well as to aminoacyl tRNA availability. In the present study, a plasmid (pPS1) carrying the promoter region of the rrnA cistron fused to the terminator region of rrnB has been used for in vitro transcription experiments. The presence of the terminators (T1 and T2) together with the fact that supercoiled DNA is found to be a highly efficient template, provide an ideal in vitro system in which to study the functional interrelationship between the two tandem promoters of E. coli rRNA cistrons. The results suggest that the rate of rRNA synthesis in E. coli cells growing in various conditions, as reflected by the availability of RNA polymerase, is primarily dependent on the properties of the two tandem rRNA promoters.

Maturation of 5-S rRNA: ribonuclease E cleavages and their dependence on precursor sequences

9-S RNA is a processing intermediate that accumulates in an RNase E- strain of Escherichia coli. It spans from the RNase III cleavage site, after 23-S rRNA, to the 3' end of the transcript and is derived from rRNA genes which do not contain tRNAs distal to 5-S rRNA. Here, we have studied the processing of 9-S RNA with ribonuclease E. RNase E cleaves 9-S RNA in two sites: one of these is three nucleotides upstream from the 5' end of 5-S rRNA, the other downstream from its 3' end. Both cleavages are probably introduced by the same enzyme, since both cleavages are thermolabile when an extract of a temperature-sensitive RNase E mutant was used for processing in vitro. In order to asses the role of 5' and 3' end precursor-specific sequences in the RNase E reaction, we isolated the molecules lacking nucleotides at the 5' or 3' end. Molecules having the 5' end of 9-S RNA but missing nucleotides from the 3' end (called 8-S RNA) were as good a substrate for RNase E as 9-S, RNA itself. However, molecules having the 3' end of 9-S RNA but the 5' end of p5 (called 7-S RNA), were less efficient substrates for RNase E. Finally, the removal of as little as seven nucleotides from the 5' end of 8-S RNA rendered it almost completely unsuitable as a substrate for RNase E.

Mutations in the rpIJ leader of Escherichia coli that abolish feedback regulation

We have isolated mutants that fail to exhibit biosynthetic feedback regulation of a rpIJ-lacZ fusion. Analysis of these mutants and of others that were isolated earlier indicates that crucial sequences for both translational feedback regulation and efficient translation lie closely intermingled in the central region of the rpIJ mRNA leader 70-195 bases upstream from the translation start of rpIJ. We suggest that our point mutations define a region of the rpIJ leader mRNA to which L10 binds in effecting autogenous translational regulation.

Regulation of the rpsU-dnaG-rpoD macromolecular synthesis operon and the initiation of DNA replication in Escherichia coli K-12

We have fused the E. coli dnaG 5' regulatory region to the TcR structural gene in the promoter probe plasmids pPV33 and pKK175-6 to demonstrate that a promoter activity is located on a 250 bp SacII-HindIII restriction fragment and that a transcription terminator, previously reported by nucleotide sequence (Smiley et al. 1982) to immediately precede the dnaG gene, acts as such in vivo. We have determined the complete nucleotide sequence of this controlling region and report: 1) tandem promoters on the same SacII-HindIII restriction fragment which promotes tet expression in the gene fusion experiments, 2) an open reading frame between these promoters and the dnaG gene which is the rpsU (ribosomal protein S21) gene, 3) a sequence homologous to the lambda nut site, 4) a possible LexA protein binding site on one of the dnaG promoters. This places the order on the E. coli genetic map at 66 min in the clockwise direction as rpsU-dnaG-rpoD which are all contained in a single macromolecular synthesis operon. We postulate a model for regulation of the initiation of DNA replication based on antitermination of the rpsU-dnaG-rpoD operon.

Protection of ribosomal RNA from kethoxal in polyribosomes. Implication of specific sites in ribosome function

In an attempt to probe the topography of 5 S, 16 S and 23 S RNAs in a functionally engaged ribosome, polysomes were probed using the structure-sensitive, guanine-specific reagent kethoxal. Reactivities of guanine residues at 38 specific ribosomal RNA sites in polysomes were compared with their corresponding reactivities in vacant 70 S ribosomes. No polysome-specific protection was seen for 5 S RNA. In 16 S RNA, positions 530, 693 or 1079, 966, 1338 and 1517 showed protection in polysomes; all of these sites have highly conserved primary and secondary structures, and include several methylated nucleotides. In 23 S RNA, polysome protection is seen at positions 277, 1071, 1475 or 2112, 2116 and 2751. We attribute polysome-specific protection either to direct contact of transfer RNA and/or messenger RNA with the protected sites or to tRNA and/or mRNA-induced changes in ribosome conformation involving the protected sites.

Identification of two genes immediately downstream from the polA gene of Escherichia coli

We have identified two genes within a 1-kilobase region immediately following the polA gene of Escherichia coli. The first, whose transcription is initiated about 150 base pairs beyond the end of the polA coding sequence, is the gene corresponding to the previously sequenced "spot 42 RNA" (B. G. Sahagan and J. E. Dahlberg, J. Mol. Biol. 131:573--592, 1979). The second, located further downstream and transcribed towards polA, is the structural gene for a 22-kilodalton polypeptide, which we have detected by using plasmid-directed protein synthesis in maxicells. Sequence analysis of this region of the E. coli genome suggests that it contains little, if any, redundant DNA.

Analysis of nutR: a region of phage lambda required for antitermination of transcription

The N gene product of coliphage lambda acts with host factors (Nus) through sites (nut) to render subsequent downstream transcription resistant to a variety of termination signals. These sites, nutR and nutL, are downstream, respectively, from the early promoters PR and PL. Thus a complicated set of molecular interactions are likely to occur at the nut sites. We have selected mutations in the nutR region that reduce the effectiveness of pN in altering transcription initiating at the PR promoter. DNA sequence analysis of three independently selected mutations revealed, in each case, a deletion of a single base pair in the cro gene. Consideration of the effect of such mutations on the extension of translation of cro message into the adjacent downstream nut region led to the identification of a consensus sequence CGCTCT(T)TAA that appears to play a role in the recognition of a host factor, possibly the NusA protein.

Primary and secondary structure in a precursor of 5 S rRNA

In order to shed some light on the mechanism of action of RNAase E, we studied primary and secondary structure in 9 S (a precursor of 5 S rRNA), p5 and 5 S rRNAs. These molecules were digested with RNAases A and T1 in the presence of a high salt concentration; conditions under which single-stranded RNA is differentially digested. The double-stranded RNA fragments were isolated and analyzed. The analyses suggested that p5 and 5 S rRNA contain a stem of ten basepairs which consists of sequences from the 5' and 3' regions of the molecule, while 9 S contains a similar stem which is three basepairs longer and includes also a bulge of three unpaired bases. The stem in the 9 S RNA contains four sites where RNA processing cleavages occur. One of the cleavage sites which leads to the formation of p5 is in a junction between single-stranded and double-stranded RNA. The 9 S RNA molecule contains another large stem of at least 15 basepairs which is derived from the 3' end of the 9 S precursor molecular; it is apparently the transcription termination stem.

Recognition of protein coding regions in DNA sequences

We give a test for protein coding regions which is based on simple and universal differences between protein-coding and noncoding DNA. The test is simple enough to use without a computer and is completely objective. The test has been thoroughly proven on 400,000 bases of sequence data: it misclassifies 5% of the regions tested and gives an answer of "No Opinion" one fifth of the time. We predict some new coding and noncoding regions in published sequences.

Escherichia coli plasmid vectors containing synthetic translational initiation sequences and ribosome binding sites fused with the lacZ gene

The construction of a series of Escherichia coli plasmid vectors suitable for assaying the effects of gene control signals fused with the E. coli lacZ gene is reported. A synthetic deoxyoligonucleotide dodecamer 5'-CATGAATTCATG GTACTTAAGTAC-5' containing two translation initiation codons (ATG) separated by an EcoRI site was ligated with a lacZ gene derivative which lacks the codons for the first eight amino acids in plasmid pMC1403 (Casadaban et al., 1980). Two ribosome-binding sequences were synthesised and inserted into the EcoRI site before an ATG, and the effects of these sequences on lacZ gene expression in vivo measured by assaying beta-galactosidase activity. The E. coli ribosomal RNA gene (rrnB) promoter, the tetracycline resistance gene promoter, and a lambda phage promoter were cloned using these plasmids. The plasmids are 9.9 kb in size, have ampicillin resistance as a selectable marker and are generally useful for the detection and in vivo assay of gene control regions.

Erythromycin resistance due to a mutation in a ribosomal RNA operon of Escherichia coli

There are seven ribosomal RNA operons (rrn operons) in Escherichia coli. A single rrn operon was amplified by use of a multicopy recombinant plasmid containing a complete rrnH operon. rrnH thereby has the potential to contribute a greater fraction of the rRNA found in ribosomes. Erythromycin-resistant mutants were isolated from cells containing the plasmid, and at least one mutation to resistance was shown to reside in rrnH on the plasmid. Erythromycin resistance was retained when a major deletion was introduced into the 16S rRNA gene and was abolished by deletions that affect the 16S and 23S rRNA genes but do not alter the 5S rRNA gene or non-rrnH DNA. Cell-free S30 protein-synthesizing extracts from cells containing the mutant plasmid have an increased resistance to erythromycin. The selection procedure used to isolate erythromycin-resistance mutations in rrnH may allow, with minor modifications, the isolation of mutations in rrn operons that change resistance of the ribosome to other antibiotics or that alter other properties of ribosomes.

Ribonuclease E is involved in the processing of 5-S rRNA from a number of rRNA transcription units

Strains of Escherichia coli having a thermosensitive RNase E produce a number of 5-S ribosomal RNA precursors at a non-permissive temperature. One of these precursors, 9-S RNA, was reported earlier [Ghora, B.K. and Apirion, D. (1978) Cell, 15, 1055-1066]. Here we show the existence of additional precursors to 5-S rRNA, originating from a number of rRNA genes. All the precursors are very similar in the first 200 nucleotides and the last part of this sequence contains the mature 5-S rRNA. Precursors that contain only these nucleotides (8-S RNA) accumulate. They probably originate from the rrn genes C, D and F which contain trailer tRNAs. The 9-S RNA precursors contain in addition a termination stem and loop structure and are derived from genes which do not contain trailer tRNA (Singh and Apirion, unpublished results). In addition, a 10-S precursor was identified. It contains distal to the 5-S rRNA a trailer tRNA, tRNAAsp, and a transcription termination signal. It is derived from the rrnF gene. The accumulation of an RNA precursor containing an RNase P site in an rne mutant suggests that the efficiency of one RNA processing enzyme depends on the activity of other RNA processing enzymes.

Nucleotide sequence of the rrnG ribosomal RNA promoter region of Escherichia coli

The primary structure of the promoter region for a ribosomal RNA transcription unit (rrnG) of Escherichia coli K12 has been determined. The sequence was obtained from 1 1.5 kbp EcoRI fragment derived from the hybrid plasmid pLC23-30. This fragment contains 455 bp preceding P1 of the rrnG promoter region and 674 bp of the rrnG 16S RNA gene. The sequence before the rrnG promoter region contains an open reading frame (ORF-BG) followed by a possible hairpin structure that resembles other known transcription terminators. The sequence of the rrnG promoter region is similar but not identical to that of rrnA and rrnB. Several minor differences between the sequences of the 16S RNA genes of rrnG and rrnB were also noted. In addition, sequences were found that could generate special structures involving the promoter regions of rrn loci. Such structures are described and their possible involvement in the regulation of ribosomal RNA synthesis is discussed.

tRNA genes are found between 16S and 23S rRNA genes in Bacillus subtilis

There are at least nine, and probably ten, ribosomal RNA gene sets in the genome of Bacillus subtilis. Each gene set contains sequences complementary to 16S, 23S and 5S rRNAs. We have determined the nucleotide sequences of two DNA fragments which each contain 165 base pairs of the 16S rRNA gene, 191 base pairs of the 23S rRNA gene, and the spacer region between them. The smaller space region is 164 base pairs in length and the larger one includes an additional 180 base pairs. The extra nucleotides could be transcribed in tRNAIIe and tRNA Ala sequences. Evidence is also presented for the existence of a second spacer region which also contains tRNAIIe and tRNA Ala sequences. No other tRNAs appear to be encoded in the spacer regions between the 16S and 23S rRNA genes. Whereas the nucleotide sequences corresponding to the 16S rRNA, 23S rRNA and the spacer tRNAs are very similar to those of E. coli, the sequences between these structural genes are very different.

Transposition of a chromosomal segment bounded by redundant rRNA genes into other rRNA genes in Escherichia coli

We have constructed several mutants of Escherichia coli which have the chromosomal segment between the directly repeated rrnB and rrnE genes deleted from the normal position and transposed into another one of the seven redundant rRNA genes. We have examples where the transposition has been into rrnC, rrnD, rrnG, and rrnH. Included in the evidence for each of these transpositions was the finding that each transposition specifically affected a different one of the seven BamHI-PstI restriction nuclease fragments known to correspond to the seven rrn genes. The transposition mutants were generally healthy, but sensitive mixed-growth experiments revealed that most of them grew somewhat more slowly than the parental control in rich medium. The maximal detrimental effect was a 4 to 5% reduction in growth rate when the transposition of the rrnB-rrnE segment was into rrnG. We have found that a rrnF gene, reported by others to be linked to malA, does not exist in our standard strain, a derivative of Cavalli Hfr. Instead of rrnF, we identified a new rrn gene, rrnH, which mapped near min 5.

The complete nucleotide sequence of 16S ribosomal RNA gene from tobacco chloroplasts

The complete nucleotide sequence of 16S ribosomal RNA gene from tobacco chloroplasts has been determined. This nucleotide sequence has 96% homology with that of maize chloroplast 16S rRNA gene and 74% homology with that of Escherichia coli 16S gene. The 3' terminal region of this gene contains the sequence ACCTCC which is complementary to sequences found at the 5' termini of prokaryotic mRNAs. The large stem and loop structure can be constructed from the sequences surrounding the 5' and 3' ends of the 16S gene. These observation demonstrate the prokaryotic nature of chloroplast 16S rRNA.

Nucleotide sequence at the end of the gene for the RNA polymerase beta' subunit (rpoC)

We have determined the DNA sequence surrounding the transcription terminator following rpoC, the gene that codes for the beta' subunit of RNA polymerase in E. coli K12. The 2044 bp sequence obtained contains the distal 335 codons of rpoC followed by a 212 bp non-coding region and a second open reading frame (ORFa) of 179 codons. The final 181 nucleotides of the sequence form the 5' end of a third open reading frame (ORFb). The in vivo 3' end of the rpoC mRNA was located by analysis of RNA/DNA hybrids cleaved with nuclease S1 (S1 mapping). These results indicated that the major transcription termination of the rplJL-rpoBC transcription unit occurs a short distance past the translation stop codon for rpoC. Four regions of symmetry, suggesting secondary structure in the mRNA, were found in the DNA sequence near the rpoC translation termination codon. The last of these hairpin structures is similar to other rho-independent transcription terminators and its 3' end coincides with the end of the rpoC mRNA as predicted by S1-mapping. Inspection of the open reading frames indicates that rpoC uses a high percentage of codons that are recognized by the major tRNA species of E. coli while ORFa and ORFb contain many codons recognized by minor tRNA species. ORFa specifies a very basic peptide.

Pausing and attenuation of in vitro transcription in the rrnB operon of E. coli

We have determined the effects of the nusA gene protein and the regulatory nucleotide guanosine tetraphosphate (ppGpp) on pausing and termination of transcription in the leader region of the rrnB operon in vitro. The leader region of rrnB contains several types of potential regulatory sequences that act at the level of RNA chain elongation and may be involved in control of bacterial growth. We have mapped a termination site, tL, located 260 bases from rrnB promoter P1. Termination at tL is dependent on the nusA protein and is enhanced by ppGpp. The DNA sequence at tL shows striking homologies with trp t', a terminator also strongly affected in vitro by the nusA protein. These in vitro results suggest that rRNA transcription in vivo may be regulated in part through an attenuation mechanism that leads to termination of rrnB chains in the leader region. In addition to tL, elongation of transcription in the leader region is affected by several pause sites that are sensitive to the concentration of ppGpp and the presence of the nusA gene protein. The location and properties of these pause sites suggest that they may also play a role in regulation of rrnB transcription through a mechanism we have termed "turnstile" attenuation. One pause site, located 90 and 91 bases from P1, is unique in that it is not normally a site for transcriptional pausing, but is dependent on simultaneous binding of polymerase at rrnB promoter P2. This leads to blockage of P1 transcripts at high RNA polymerase densities and may provide an additional locus for regulation of rrn transcription.

Processing of procaryotic ribonucleic acid

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