Interaction of RNA polymerase from Escherichia coli with DNA. Analysis of T7 DNA early-promoter sites

Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli

Chemical modifications of RNA 5'-ends enable "epitranscriptomic" regulation, influencing multiple aspects of RNA fate. In transcription initiation, a large inventory of substrates compete with nucleoside triphosphates for use as initiating entities, providing an ab initio mechanism for altering the RNA 5'-end. In Escherichia coli cells, RNAs with a 5'-end hydroxyl are generated by use of dinucleotide RNAs as primers for transcription initiation, "primer-dependent initiation." Here, we use massively systematic transcript end readout (MASTER) to detect and quantify RNA 5'-ends generated by primer-dependent initiation for ∼410 (∼1,000,000) promoter sequences in E. coli The results show primer-dependent initiation in E. coli involves any of the 16 possible dinucleotide primers and depends on promoter sequences in, upstream, and downstream of the primer binding site. The results yield a consensus sequence for primer-dependent initiation, YTSS-2NTSS-1NTSSWTSS+1, where TSS is the transcription start site, NTSS-1NTSS is the primer binding site, Y is pyrimidine, and W is A or T. Biochemical and structure-determination studies show that the base pair (nontemplate-strand base:template-strand base) immediately upstream of the primer binding site (Y:RTSS-2, where R is purine) exerts its effect through the base on the DNA template strand (RTSS-2) through interchain base stacking with the RNA primer. Results from analysis of a large set of natural, chromosomally encoded Ecoli promoters support the conclusions from MASTER. Our findings provide a mechanistic and structural description of how TSS-region sequence hard-codes not only the TSS position but also the potential for epitranscriptomic regulation through primer-dependent transcription initiation.

The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: implications for transcription start-site selection

Bacterial transcription is initiated after RNA polymerase (RNAP) binds to promoter DNA, melts ~14 bp around the transcription start site and forms a single-stranded "transcription bubble" within a catalytically active RNAP-DNA open complex (RP(o)). There is significant flexibility in the transcription start site, which causes variable spacing between the promoter elements and the start site; this in turn causes differences in the length and sequence at the 5' end of RNA transcripts and can be important for gene regulation. The start-site variability also implies the presence of some flexibility in the positioning of the DNA relative to the RNAP active site in RP(o). The flexibility may occur in the positioning of the transcription bubble prior to RNA synthesis and may reflect bubble expansion ("scrunching") or bubble contraction ("unscrunching"). Here, we assess the presence of dynamic flexibility in RP(o) with single-molecule FRET (Förster resonance energy transfer). We obtain experimental evidence for dynamic flexibility in RP(o) using different FRET rulers and labeling positions. An analysis of FRET distributions of RP(o) using burst variance analysis reveals conformational fluctuations in RP(o) in the millisecond timescale. Further experiments using subsets of nucleotides and DNA mutations allowed us to reprogram the transcription start sites, in a way that can be described by repositioning of the single-stranded transcription bubble relative to the RNAP active site within RP(o). Our study marks the first experimental observation of conformational dynamics in the transcription bubble of RP(o) and indicates that DNA dynamics within the bubble affect the search for transcription start sites.

Mechanism of stimulation of ribosomal promoters by binding of the +1 and +2 nucleotides

The rate of transcription of Escherichia coli ribosomal RNA promoters is central to adjusting the cellular growth rate to nutritional conditions. The +1 initiating nucleotide and ppGpp are regulatory effectors of these promoters. The data herein show that in vitro transcription is also regulated by the +2 nucleotide. Both the +1 and +2 nucleotides act by driving polymerase into an altered conformation rather than by increasing the lifetime of transcription complexes. The unique design of the ribosomal promoters may stabilize a distorted state of polymerase that is relieved by the binding of the two nucleotides required for transcription initiation.

Synthesis of in vitro Co1E1 transcripts with 5'-terminal ribonucleotides that exhibit noncomplementarity with the DNA template

A region that forms the S1 nuclease site in Co1E1 DNA is shown to code for an in vitro transcript, called S1 RNA-B, which contains a 5'-terminal GTP residue that exhibits noncomplementarity with the template's DNA sequence. The synthesis of S1 RNA-B initiates four bases upstream from the start point for S1 RNA-C. The initial four bases in S1 RNA-B and S1 RNA-C are identical. The relative synthesis of S1 RNA-B to S1 RNA-C is sensitive to the concentration of GTP, a substrate that is required for elongation past the +4 position in S1 RNA-C. Dinucleotides that are expected to only initiate synthesis of S1 RNA-C yield two transcripts that appear to initiate from the S1 RNA-C and S1 RNA-B start sites. In vitro studies involving other Co1E1 transcripts, RNA-B and RNA-C, provide similar observations concerning the noncomplementary initiation phenomenon. A model involving transcriptional slippage is suggested to explain the noncomplementary initiation phenomenon. The model proposes that the cycling reaction of Escherichia coli RNA polymerase produces tetranucleotides that are transposed to nearby upstream sequences for priming transcription.

Oligonucleotides complementary to a promoter over the region -8...+2 as transcription primers for E. coli RNA polymerase

Primer-dependent transcription by E. coli RNA polymerase on T7 promoter A2 has been studied. Synthetic deoxyribonucleotides complementary to the promoter over the region -8...+2 were taken as primers. A ribonucleoside residue was present at the 3'-end of some of these oligonucleotides. The octanucleotide complementary to the region -8...-1 appeared to be an active primer. Oligonucleotides having lengths from 3 to 6 nucleotide residues complementary to the promoter over the region -4...+2 also exhibited primer activity. The latter was some 5-10 times greater in the case of oligonucleotides having a ribonucleoside residue at the 3'-end. Oligonucleotides which on complementary binding do not reach the center of phosphodiester bond synthesis, as well as the decanucleotides (-8...+2) and octanucleotides (-6...+2) of both the ribo- and deoxyribo-series were inactive as primers.

Properties of P3 esters of nucleoside triphosphates as substrates for RNA polymerase from Escherichia coli

P3-[(2,4-Dinitrophenyl)amino]ethyl (DNPNHEt) and P3-methyl phosphate esters of nucleoside 5'-triphosphates have been synthesized. Their properties as substrates in the initiation and elongation steps of transcription have been examined by using RNA polymerase from Escherichia coli and poly[d(A-T)] or T7 DNA as templates. It is shown that transcription can be initiated by ATP-EtNHDNP and that 2,4-dinitrophenyl residues are incorporated at the 5' end of the RNA molecules. Steady-state kinetic experiments of abortive initation on promoters A1 and A3 of T7 DNA revealed that ATP-EtNHDNP, ADP-EtNHDNP, and ATP-OCH3 have lower Km values and markedly reduced Vmax values compared to those of ATP. The two classes of esters, NTR-EtNHDNP and NTP-OCH3, were found to differ regarding their utilization as substrates for elongation. Both ATP-OCH3 and UTP-OCH3 are substrates for transcription. However, only the pyrimidine derivatives of NTP-EtNHDNP are elongation substrates which release DNPNHEt-PP upon utilization. This dramatic difference between the purine and pyrimidine derivatives of NTP-EtNHDNP reflects a selective process in the transcriptional complex for purines and pyrimidines.

Localization of the binding sites of prokaryotic and eukaryotic RNA polymerases on simian virus 40 DNA

The binding sites of calf thymus RNA polymerase (B) II, wheat germ RNA polymerase B and of the Escherichia coli RNA polymerase were mapped on the simian virus 40 genome by observation of enzyme-linear DNA complexes by electron microscopy. Three to four major sites and several minor sites are observed for each enzyme; common binding sites for the three enzymes are found in positions 0.17, 0.53 and 0.90 of the viral physical map. Initiation complexes with these enzymes can be stabilized with specific ribodinucleotides and a single ribonucleoside triphosphate. Whereas ApA and ATP greatly enhances the binding of the E. coli enzyme at position 0.17, they stabilize the binding of the eukaryotic enzyme at many sites, some of them located in close proximity of the origin of replication.

The influence of ribonucleoside triphosphates, and other factors, on the formation of very-salt-stable RNA-polymerase . su+III-tRNA(tRNATyr)-promoter complexes

The formation of a stable RNA-polymerase . su+III-tRNA-promoter complex was found to require sigma factor and the incorporation of ribonucleoside triphosphates which match the 5' sequence of the su+III tRNA transcript. This complex, stable to at least 2 M KCl, can be retained on a Millipore filter. Its formation closely parallels the extent of transcription obtained from the su+III tRNA promoter in response both to increasing ionic strength and to temperature during incubation of RNA polymerase with the DNA. The RNA-polymerase . DNA complex retained during this assay therefore appears to relate directly to that formed during promoter-directed transcription. The formation of RNA-polymerase . su+III-tRNA-promoter complexes is sensitive to the presence of ppGpp.

Transcription of bacteriophage T4 DNA in vitro: selective initiation with dinucleotides

The transcription products of phage T4 DNA in vitro are separated on polyacrylamide gels. The influence of salt, polymerase, triphosphate concentration and glucosylation on the RNA synthesis are shown. Individual transcripts are initiated selectively with dinucleotides and a single triphosphate. This technique allows the prediction of the initiation sequences of several T4 transcripts.

Electron microscopy analysis of the interaction between Escherichia coli DNA-dependent RNA polymerase and the replicative form of phage fd DNA. 1. Mapping of the binding sites

The interaction of Escherichia coli DNA-dependent RNA polymerase (EC 2.7.7.6) with the replicative form of the DNA from the filamentous coliphage fd cleaved by the restriction endonuclease HindII has been studied by electron microscopy at low and high ionic strength. In the presence of ATP or GTP, and heparin, RNA polymerase binds to fd replicative-form DNA at a few specific sites which have been mapped. The map was oriented so that transcription is from right to left. Three main GTP initiator sites are found at 15%, 82% and 94% of the genome length. One main ATP initiator site is found which cannot be mapped with the same accuracy, and which is localized between 38% and 50%. In the absence of initiator triphosphates and heparin, the binding of the enzyme to fd DNA is much more heterogeneous and therefore the mapping is more difficult. Nevertheless it seems that the preferential binding regions correspond to the specific sites mapped in the presence of GTP or ATP. The mean number of polymerase molecules bound to DNA as a function of the molecular ratio enzyme to DNA present in the mixture has been determined. From these results a binding isotherm can be obtained. The apparent equilibrium constant (K approximately 10(9) M-1) which is derived certainly represents an under-estimated value, as discussed.

Interaction of RNA polymerase with promoters from bacteriophage fd

Replicative form DNA of bacteriophage fd, which had been fragmented with the restriction endonuclease II from Hemophilus parainfluenzae (endo R- HpaII), was reacted with Escherichia coli RNA polymerase; the resulting stable preinitiation complexes were analysed using the filter binding assay followed by gel electrophoresis. At 120mM KCL the first-order rate constants for complex decay were determined to be 10(-2)-10(-6)s-1. The second-order rate constants for complex formation were found to be about 10(6) -10(7) M-1 s-1. From these values association constants for the individual promoters were calculated to be 2 x 10(-8) -2 x 10(-11) M-1. The rate of formation and the stability of promoter complexes was enhanced in superhelical DNA. No evidence was found for stable promoter-specific closed complexes consisting of enzyme and helical DNA. This and the kinetic data suggest that the unwinding of base pairs is already important early in promoter selection, and not only for the formation of the final open complex. The initiation of RNA synthesis form the preinitiation complex was faster than complex dissociation and complex formation for all promoters. Consequently, the initiation efficiency of a promoter is determined by the rate of complex formation, and not by its 'affinity' for the enzyme. No correlation was found between the relative order of the fd promoters for the binding and the dissociation reaction. This is explained by different structural determinants, for the two reactions, which are located in different parts of the promoter DNA.

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.