Nucleotide sequence in the promoter region of the Escherichia coli tyrosine tRNA gene

Odd RNA polymerases or the A(B)C of eukaryotic transcription

Pioneering studies on eukaryotic transcription were undertaken with the bacterial system in mind. Will the bacterial paradigm apply to eukaryotes? Are there promoter sites scattered in the eukaryotic genome, and sigma-like proteins? Why three forms of RNA polymerase in eukaryotic cells? Why are they structurally so complex, in particular RNA polymerases I and III, compared to the bacterial enzyme? These questions and others that were raised along the way are evoked in this short historical survey of odd RNA polymerases studies, with some emphasis on the contribution of these studies to our global understanding of eukaryotic transcription systems. This article is part of a Special Issue entitled: Transcription by Odd Pols.

The hisR locus of Salmonella: nucleotide sequence and expression

In S. typhimurium, the hisR locus is defined by mutations causing reduced levels of the histidine transfer RNA. As a preliminary step in the analysis of the hisR mutants, a 972 bp DNA fragment containing the histidine tRNA gene from wild-type Salmonella was cloned and completely sequenced. This analysis revealed the existence of a tRNA gene cluster which, in addition to the tRNAHis gene, includes the genes for tRNALeu1, tRNAPro1 and a tentative tRNAArgCGG. All four tRNA genes are present as single copies and are separated by spacer sequences ranging from 20 to 53 bp in length. The gene cluster is efficiently transcribed in vitro by E. coli RNA polymerase and yields a transcript, approximately 480 nucleotides long, which contains all four tRNA sequences. This tetrameric precursor can be processed to 4S RNA in vitro with a wild-type Salmonella extract, but not with an extract prepared from a hisU (RNase P) mutant. Using portions of the tRNA gene cluster as specific hybridization probes, various processing intermediates were shown to accumulate in vivo in the hisU mutant. Most of these RNAs are monomeric precursors only a few nucleotides longer than the respective mature tRNA species.

PpGpp regulates the binding of two RNA polymerase molecules to the tyrT promoter

Bacterial promoters differ in the number of RNA polymerase molecules that bind to form a filterable polymerase-promoter complex. We show that two holoenzyme molecules interact with the tyrT promoter, probably as a dimer. This interaction is inhibited by ppGpp. By contrast a single holoenzyme monomer suffices for complex formation at the lacUV5 promoter. We propose that In vivo promoter selection by monomeric and dimeric forms of the enzyme could coordinate the synthesis of stable RNA with that of mRNA and could also account in part for the switch in transcriptional selectivity during the stringent response.

Dual function transcripts specifying tRNA and mRNA

A cluster of four tRNA genes in Escherichia coli is co-transcribed with an adjacent gene encoding elongation factor Tu. The resultant transcript that specifies both structural (tRNA) and informational (mRNA) RNA may not be an uncommon occurrence and has interesting regulatory implications.

Structure and distribution of inverted repeats (Palindromes). I. Analysis of DNA of Drosophila melanogaster

The size and distribution of renatured inverted repeats (palindromes) in D. melanogaster DNA were studied by electron microscopy (EM). The results of these studies differ from the previously published observations regarding the number, distribution and the size of inverted repeats (ir) present in DNA. -1. In contrast to the previous published observation almost all (96%) of the ir were found in crowded clusters. The DNA strands with clustered palindromes contained 2-21 palindromes (4-42 ir), with an average of 7.25 palindromes (14.5 ir) per strand. No correlation could be found between the length of the DNA strands and the number of ir per strand. -2, Also contrary to some previously published results, most (80%) of the ir formed on renaturation unlooped palindromes and these were always clustered. Looped palindromes (hairpins, formed by renaturation of ir separated by a non-homologous sequence long enough to be seen in EM as single-stranded loop) were found 1-2 per DNA strand, as part of clusters or as solitary palindromes in a DNA strand. The average spacing length (inside clusters) between centers of all palindromes was 2.349 kb, and between centers of looped palindromes 7.6 kb. - 3. The length of the ir was found to be smaller than documented in most of the previously published results. The majority, 80-90%, of the ir found in the unlooped and looped palindromes, respectively, belonged to one main-size class with a range of 30-210 bp and an average length of 100 bp, but longer ir were also observed. The average length of the ir in unlooped palindromes was 124 bp, in looped 244 bp, and the total average was 148 bp - 4. It was calculated that there are about 30,000 palindromes (60,000 ir) in the D, melanogaster genome, of which about 24,000 are unlooped and 6,000 looped, with the spacing between centers of all palindromes averaging about 4.4 kb in length.

Sequence of the distal tRNA1Asp gene and the transcription termination signal in the Escherichia coli ribosomal RNA operon rrnF(or G)

Several DNA fragments carrying tRNA genes have been cloned from EcoRI endonuclease digests of Escherichia coli DNA. Using cloned DNA, the sequence of the region around the distal gene for tRNA1Asp (F(or G)) in the E. coli ribosomal RNA operon [rrnF(or G)] has been determined. In the distal portion of rrnF(or G), the genes for 23S, 5S rRNA and tRNA1Asp (F(or G)) are located in that order and separated by intergenic spacers of 93 and 52 base pairs, respectively. A possible hairpin structure, with its center between the 22nd and 23rd base pair downstream from the 3'-end of the tRNA1Asp(F(or G)) gene, followed by a sequence of eight thymidine residues was identified as the transcription termination signal for rrnF(or G). The termination is rho-independent, at least in vitro, and occurs within the region of the contiguous thymidine residues. A possible promoter for a protein gene is present about 50 base pairs downstream from the rrnF(or G) terminator.

Promoter mutations in the transfer RNA gene tyrT of Escherichia coli

The DNA sequences for nine independent promoter mutants of a tyrosine tRNA gene, tyrT of Escherichia coli, are reported. The nine mutations involve six transitions, two transversions, and one deletion. They are located at four different sites in the first 30 base pairs preceding the start point of transcription. The changes found are: a T.A to A.T transversion at position -8 (two mutants); a T.A to C.G transition at position -8 (three mutants); a T.A to C.G transition at position -13 (two mutants); a T.A to C.G transition at position -16 (one mutant); and a deletion of a G.C base pair at position -26/27 (one mutant). Four of the five different mutant tyrT promoters have alterations at positions that might have been expected from DNA sequence studies with other prokaryote promoters. One of these mutants (a G.C deletion at position -26/27) occurs in a stretch of eight consecutive G.C base pairs which may be characteristic of stable RNA promoters.

Nucleotide sequence of the ribosomal protein gene cluster adjacent to the gene for RNA polymerase subunit beta in Escherichia coli

The 3072-nucleotide-long sequence of a segment from the 88-min region of the Escherichia coli chromosome has been determined. The sequence covers the genes for ribosomal proteins L11 (rplK), LI (rplA), L10 (rplJ), and L7/L12 ((rplL), and the 5' end of the gene for the beta subunit of RNA polymerase (rpoB), along with the presumed regulatory regions for these genes. The probable locations of the promoter for the first two genes (the L11 operon) and the promoter for the latter three genes (the proximal part of the beta operon) have been identified. We have also found that the four ribosomal protein genes preferentially use codons that are recognized efficiently by the most abundant tRNA species. These and other features of the sequence results are discussed in relation to available information obtained from both in vitro and in vivo experiments on the expression of these ribosomal and RNA polymerase subunit genes.

Total synthesis of a gene

The method developed for the total synthesis of a given DNA containing biologically specific sequences consists of the following. The DNA in the double-stranded form is carefully divided into short single-stranded segments with suitable overlaps in the complementary strands. All the segments are chemically synthesized starting with protected nucleosides and mononucleotides. The 5'-OH ends of the appropriate oligonucleotides are then phosphorylated with the use of [y-32P]ATP and polynucleotide kinase. A few to several neighboring oligonucleotides are then allowed to form bihelical complexes in aqueous solution, and the latter are joined end to end by polynucleotide ligase to form covalently linked duplexes. Subsequent heat-to-tail joining of the short duplexes leads to the total DNA. The methods are described for the construction of a biologically functional suppressor transfer RNA gene. The total work involved (i) the synthesis of a 126-nucleotide-long bihelical DNA corresponding to a known precursor to the tyrosine suppressor transfer RNA, (ii) the sequencing of the promoter region and the distal region adjoining the C-C-A end, which contained a signal for the processing of the RNA transcript, (iii) total synthesis of the 207 base-pair-long DNA, which included the control elements, as well as the Eco R1 restriction endonuclease specific sequences at the two ends, and (iv) full characterization by transcription in vitro and amber suppressor activity in vivo of the synthetic gene.

DNA sequence for a low-level promoter of the lac repressor gene and an 'up' promoter mutation

The promoter for a weakly expressed constitutive gene, the lactose repressor gene (lacI), has been sequenced, along with an 'up' promoter mutation Iq. The 10-fold enhancement in I expression found in Iq is the result of a single base change at position -35. To facilitate the sequencing, the lacI gene was cloned in a small plasmid.

Structure of a promoter for T7 RNA polymerase

We have determined the nucleotide sequence of a Hpa II restriction fragment of the phage T7 DNA containing a promoter for the phage-specified RNA polymerase. (Hpa II is a restriction endonuclease from Haemophilus parainfluenzae.) Mapping of the Hpa II restriction fragments on the T7 genome shows this promoter to be the second of tandem promoters separated by approximately 170 base pairs that begin transcription by the T7 RNA polymerase at approximately 15% of the genome. Features of the sequence involved in recognition by the T7 RNA polymerase are discussed and include the following region of hyphenated 2-fold symmetry (boxed regions are related through a 2-fold axis of symmetry at the center of the sequence shown). (See article). This sequence includes the initiation site, since the message transcribed from this fragment begins pppG-G-G-A. Combination of our results with work of others has permitted this fragment to be mapped at the junction of T7 genes 1 and 1.1. The RNA transcribed from this fragment begins within gene 1 and contains the RNase III cleavage site that lies between genes 1 and 1.1. This sequence is compared to other processing sites in T7 early message.

A model of promoter recognition along the two helical grooves of DNA

A speculative model based on published sequences to explain the specific binding of RNA polymerase of E. coli to promoters is suggested: (see article). A fragment 24 base pairs long to the left of the initiation site must not contain the G's in the positions indicated by the circles and must contain T's (or G's) in the positions marked by the squares. In most known cases mutual disposition of the circle and square patterns is as shown above. In one case (the fd G3 promoter) the pattern of squares is shifted by 4 base pairs to the right relative to the pattern of universal non-G's (circles).

Structure of Caulobacter deoxyribonucleic acid

The deoxyribonucleic acid of the dimorphic bacterium Caulobacter crescentus contains a component that renatures with rapid, unimolecular kinetics. This component was present in both swarmer and stalked cells and exhibited the sensitivity to endonuclease S1 expected for hairpin loops. Double-stranded side branches between 100 and 600 nucleotide pairs in length were visible in electron micrographs of rapidly reassociating deoxyribonucleic acid isolated by hydroxyapatite chromatography. No extrachromosomal elements were found in spite of systematic attempts to detect their presence. These results indicate that the rapidly reassociating fraction derives from inverted repeat sequences within the chromosome and not from cross-links or plasmids. We estimate that there are approximately 350 inverted repeat regions per Caulobacter genome. The kinetic complexity of Caulobacter deoxyribonucleic acid, however, is no greater than that of other bacteria.

Interaction of RNA polymerase from Escherichia coli with DNA. Effect of temperature and ionic strength on selection of T7 DNA early promoters

Factors influencing promoter site selection by Escherichia coli RNA polymerase were investigated using T7 DNA as template. The utilization of the three major early promoters A1, A2 and A3, was followed by processing the RNA transcripts with RNAase III, which generates the three corresponding initiator RNA fragments. The three promoters proved to be functionally distinct. A strong differential effect of temperature and ionic strength on promoter selection was observed. The transition temperature of promoters A1, A2 and A3 was measured directly by preincubating, at different temperatures, RNA polymerase and T7 DNA, with primer-substrate combinations which selected each site independently. The transition temperature of the three sites was markedly different. Promoter A3 was used predominantly at low temperature, whereas A1 or A2 promoters were gradually activated by increasing the temperature. The temperature response curves were strongly dependent upon the salt concentration. On the other hand, challenge experiments with rifampicin or poly (inosinic acid) showed that, once preinitiation complexes are formed by incubating RNA polymerase with DNA at 37 degrees C, the three sites A1, A2 and A3 promote chain initiation with equal efficiency and at the same rate.

Influence of DNA acidification on DNA premelting and template properties

Acidification of a T7 DNA sample was found to be partly irreversible as ultraviolet difference spectra measured at various sub-melting temperatures were different from those observed for a 'normal' DNA sample. This implies some subtle conformational change which is not reversed by return to neutral pH. In the same conditions, only poly(purine)-poly(pyrimidine) polymers behaved in a different manner, during premelting, according to whether they were previously acidified or not. The properties of acidified and reneutralized T7 DNA were also investigated for Escherichia coli RNA polymerase binding and transcription. An inhibition of RNA synthesis and chain initiation was observed. The results suggest that the binding of the enzyme is affected. RNA synthesized is specific but there is a decrease in the number and in the stability of the RNA-polymerase-DNA complexes.

Sequence of promoter for coat protein gene of bacteriophage fd

The nucleotide sequence in the promoter region for the coat protein gene of phage fd has been determined. This sequence contains an endonuclease R-Hha cleavage site at the fifteenth nucleotide upstream from the RNA start site. Cleavage results in loss of promoter function. Comparison with the sequence of another fd promoter indicates that the longest sequence common to both was TATAAT in the region in which RNA polymerase forms a stable initiation complex.

Promoter-dependent transcription of tRNAITyr genes using DNA fragments produced by restriction enzymes

Two DNA fragments prepared from the transducing bacteriophage strains ø80psuIII+ and ø80hpsuIII+,- by digestion with restriction enzymes contain one tyrosine tRNA gene (suIII+) and two tyrosine tRNA genes (suIII+, su-) in tandem, respectively, a single promoter in both cases, and some additional DNA regions at the two ends of both. Using these fragments, we have studied characteristics of the promoter-dependent transcription of the tyrosine tRNA genes. The promoter-dependent transcripts were shown to correspond to the expected tRNA precursors. Exposure of the transcript from the single gene fragment to an S100 extract from Escherichia coli gave, via intermediates, 4S material which was active in enzymatically accepting tyrosine and contained some modified bases.

Studies on bacteriophage fd DNA. III. Nucleotide sequence preceding the RNA start-site on a promoter-containing fragment

A short DNA fragment containing a strong promoter was isolated from phage fd replicative form DNA with the use of restriction endonucleases, and the sequence of 110 nucleotides in the region preceding the RNA start-site was determined. The sequence was : (5') CGGTCTGGTTCGCTTTGAGGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATCGAATTCGCTTTGCTTCTGACTATAATAGACAGG (3').

Determination of the sequences of 18 nucleotides from the 5'-end of the 1-strand and 15 nucleotides from the 5'-end of the r-strand of T7 DNA

The sequences of 18 nucleotides from the 5'-end of the 1-strand and 15 nucleotides from the 5'-end of the r-strand of T7 bacteriophage DNA have been determined to be pT-C-T-C-A-C-A-G-T-G-T-A-C-G-T-C-C-C (1-strand) and pA-G-G-G-A-C-A-C-A-G-C-G-C-T-C (r-strand). The 5'-termini of whole DNA or separated strands were kinased using polynucleotide kinase and (gamma-32-P) rATP. The DNA was partially digested with pancreatic DNase and the fragments were separated by two dimensional electrophoresis and homochromatography. To complete the sequence, snake venom phosphodiesterase digestions of these fragments were carried out. The relationship of these sequences to the proposed cleavage of concatemeric DNA during DNA replication is discussed.

Sequence of the OR operator of phage lambda

A sequence of 79 nucleotides from the lambda OR operator is obtained by primed transcription of repressor protected DNA fragments. The sequence contains the primary repressor binding site plus partial duplications which can be interpreted as secondary repressor binding sites.

Sequence of the PR promoter of phage lambda

The RNA polymerase binding site from the lambda PR promoter was isolated and sequenced. This DNA fragment contains the transcription initiation site and shares 25 nucleotides with OR. The sequence preceding the initiation site suggests that the promoter recognition site is not identical with the tight binding and initiation site.

Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter

Escherichia coli RNA polymerase (EC 2.7.7.6), bound in a tight complex at an early T7 promoter, protects 41 to 43 base pairs of DNA from digestion by DNase. I. The protected DNA fragment contains both the binding site for RNA polymerase and the mRNA initiation point for the promoter. The sequence of the DNA fragment and the sequence of the mRNA that it codes for are presented here. A seven-base-pair sequence, apparently common to all promoters, is implicated in the formation of a tight binary complex with RNA polymerase.

On the statistical significance of primary structural features found in DNA-protein interaction sites

Probabilities of occurrence for a number of the symmetries and other sequence regularities found in DNA-protein interaction site sequences have been calculated for segments of random DNA sequence. Results show that many of the symmetrical and repetitive features seen in these interaction sites are likely to have occured by chance. Other features are so unlikely to have occurred by chance that they are probably involved in the DNA-protein interaction processes.

The nucleotide sequence of an RNA polymerase binding site on bacteriophage fd DNA

The nucleotide sequence of the RNA polymerase binding site at a promotor on fd RF DNA has been determined in comparison with the starting sequence of RNA initiated at this promoter. The RNA polymerase binding site contained the startpoint of transcription in the centre and a region with twofold symmetry in the non-transcribed part.

Nucleotide sequence of an RNA polymerase binding site from the DNA of bacteriophage fd

The primary structure of a strong RNA polymerase binding site in the replicative form DNA of phage fd has been determined by direct DNA sequencing. It is: (see article). The molecule contains regions with 2-fold symmetry and sequence homologies to promoter regions from other DNAs. The startpoint of transcription is located in the center of the binding site.