The in vitro transcription units of bacteriophage phiX174. III. Initiation with specific 5' end oligonucleotides of in vitro phiX174 RNA

Mapping the initiation sites of in vitro transcripts of bacteriophage S13

Analysis of in vitro run-off transcripts synthesized by Escherichia coli RNA polymerase holoenzyme on linearized bacteriophage S13 DNA templates revealed five major transcription initiation sites. The sites, located at positions 45, 982, 1823 (1827), 4876 and 5211, are each within the boundaries of promoters or putative promoters previously mapped by footprinting and RNA polymerase binding analyses. They correspond to initiations at promoters upstream of the A, B, and D genes, and at a medium-affinity and a high-affinity RNA polymerase binding site P5211, respectively. Sequence analysis of the 5'-ends of two transcripts confirmed their initiation with pppA at nt 982 and nt 5211, the B gene and high-affinity binding site P5211, respectively. Some of the transcripts initiated at nt 4876 and nt 5211 terminated at nt 64, providing direct evidence of the functionality of a p-independent termination site at nt 64.

Mapping of RNA polymerase binding sites in the H/A gene region of bacteriophage S13 by footprinting and exonuclease III analysis

The H/A gene region of the bacteriophage S13 genome (map positions 4597 to 289) was analyzed for Escherichia coli RNA polymerase-binding sites by combined DNase I footprinting, exonuclease III analysis and DNA sequencing. Two high-affinity binding sites were identified, one corresponding to the A gene promoter at position 5384 to 56, overlapping the H/A intergenic region at position 1 to 63, the other at position 5171 to 5230, at the 3'-end of the H gene. A medium-affinity RNA polymerase binding site was mapped at position 4810 to 4850 in the middle of the H gene upstream of a low-affinity site at position 5280 to 5330. The studies complete footprinting analyses of the S13 genome from position 4597 to 2198 and in combination with previous studies on transcription provide definitive evidence on the position of the A gene promoter in S13 and the closely related phage psi X174.

Mapping the B and D gene promoters of bacteriophage S13 by footprinting and exonuclease III analysis

The region of the bacteriophage S13 genome which contains the B, K, and C genes and most of the A, D, and E genes (map positions 627 to 2198) was analyzed for Escherichia coli RNA polymerase-binding sites by combined DNase I footprinting, exonuclease III analysis, and DNA sequencing. Two high-affinity binding sites that correspond to the B and D gene promoters were mapped at positions 936 to 995 and 1779 to 1848, respectively. Positions 936 to 995 are in gene A, preceding the B gene, and positions 1779 to 1848 are in gene C, just preceding the D gene. In addition, two lower-affinity binding sites were identified at positions 1527 to 1538 and 1705 to 1756 preceding the C and D genes, respectively. The footprinting studies described here, in combination with previous studies on transcription, provide definitive evidence on the position of the B and D gene promoters in S13 and the closely related phage phi X174.

Localization of Escherichia coli RNA polymerase-binding sites on bacteriophage S13 replicative form I DNA by protection of restriction enzyme cleavage sites

Protection of restriction endonuclease cleavage sites by Escherichia coli RNA polymerase bound to the replicative form I of bacteriophage S13 DNA has been used to identify a number of regions of RNA polymerase binding. Digestion with HincII, AluI, HinfI, or HaeIII, under conditions optimized for "open" complex formation, revealed 12 regions of RNA polymerase binding. Based on differential salt sensitivities, five of the regions were classified as strong or tight binding sites. These were located before genes A (two sites), B, and D and at the 5' end of gene F. The seven regions which exhibited weaker binding were located at the 5' end of gene C (two sites), in the middle of gene D, just before and at the 3' end of gene F, at the 5' end of gene G, and in the middle of gene H. The sites before genes B and D coincide with sites previously identified as promoters in bacteriophage phi X174. One of the sites before gene A, that at nucleotides 5175-5211, represents a new putative promoter site in bacteriophage S13 and phi X174 located before the previously identified A gene promoter at nucleotides 10-45.

Identification of initiation sites for the in vitro transcription of rRNA operons rrnE and rrnA in E. coli

The transcription initiation sites of E. coli rRNA operons were determined using various DNA fragments derived from transducing phage lambda metA20 carrying rrnE and from hybrid plasmid pLC19-3 carrying rrnA. In vitro transcription products were analyzed for their 5' end sequences and their oligonucleotide compositions. The results are in full agreement with the nuceotide sequences of the DNA templates described in an accompanying paper (de Boer, Gilbert and Nomura, 1979) and allow us to make the following conclusions. First, there are two transcription, start sites on each of the rRNA operons; they are 109 bp apart in the case of rrnE and 117 +/- 1 bp aprart in rrnA. Second, the first start site is 283 bp upstream from the m16S rRNA coding region in the case of rrnE, while is 291 bp upstream in rrnA. Initiation starts with ATP in both cases. Finally, the second start sites are 174 and 174 +/- 1 bp from the m16S rRNA genes in rrnE and rrnA, respectively. Initiation starts with CTP in both cases. We have also shown that in the present in vitro transcription system, guanosine tetraphosphate (ppGpp) inhibits the synthesis of full-sized RNAs from both start sites in each rRNA operon.

Tandem promoters direct E. coli ribosomal RNA synthesis

To determine the special feature of ribosomal RNA promoters that might account for the highly efficient and regulated synthesis of rRNA in E. coli, we have analyzed the beginnings of two ribosomal RNA operons, rrnD and rrnX. DNA sequences for 425 bp preceding those specifying mature 16s rRNA are reported. In vitro transcription of restriction endonuclease fragments containing this region from either operon reveals the presence of two promoters about 110 nucleotides apart; they are denoted P1 and P2. RNA synthesis from P1 is initiated with GTP at position -284 (relative to 16s sequences) in rrnD and with ATP at position -285 in rrnX. At P2, the RNA starts with CTP primarily at position-176 in both operons. The DNA sequences of the two operons are identical for 231 bp preceding the 16s rDNA (including a substantial region around P2); they then diverge almost completely, except for a notable 18 bp homology just preceding the transcription start site for P1. Certain sequences implicated in the recognition of promoters by E. coli RNA polymerase are clearly identifiable in both P1 and P2; other features include an extended region preceding P1 which is strikingly rich in AT base pairs. Possible mechansims by which these tandem promoters contribute to the high frequency of rRNA transcription and to the differential expression of the E. coli rrn operons are discussed.

The nucleotide sequence of two restriction fragments located in the gene AB region of bacteriophage S13

The nucleotide sequence of a double stranded DNA fragment from the gene AB region of bacteriophage S13 DNA has been determined. The fragment was isolated as two adjacent shorter fragments by cleavage of S13 replicative form (RF) DNA with restriction endonuclease III from Hemophilus aegyptius. The strands of the fragments were separated electrophoretically and hydrolyzed with T4 endonuclease IV to yield short oligonucleotides which were then sequenced by partial exonuclease digestion. The complete nucleotide sequence of the restriction fragments was obtained by ordering the inter- and intrastrand overlapping oligonucleotide sequences. The adjacent fragments were 190 nucleotides in length. The sequences included a HindII site, an AluI site and two sequences which may be possible transcription initiation sequences, one with an adjacent sequence homologous to the canonical promoter site sequence T-A-T-Pu-A-T-Pu. Examination of the three possible reading frames for translation of the sequence revealed only one possible complete translation product. The postulated partial sequence of gene A protein has a highly positively charged arginine-rich area which may have importance in DNA binding.