Transcription at bacteriophage T4 variant late promoters. An application of a newly devised promoter-mapping method involving RNA chain retraction

Transcription of the T4 late genes

This article reviews the current state of understanding of the regulated transcription of the bacteriophage T4 late genes, with a focus on the underlying biochemical mechanisms, which turn out to be unique to the T4-related family of phages or significantly different from other bacterial systems. The activator of T4 late transcription is the gene 45 protein (gp45), the sliding clamp of the T4 replisome. Gp45 becomes topologically linked to DNA through the action of its clamp-loader, but it is not site-specifically DNA-bound, as other transcriptional activators are. Gp45 facilitates RNA polymerase recruitment to late promoters by interacting with two phage-encoded polymerase subunits: gp33, the co-activator of T4 late transcription; and gp55, the T4 late promoter recognition protein. The emphasis of this account is on the sites and mechanisms of actions of these three proteins, and on their roles in the formation of transcription-ready open T4 late promoter complexes.

The C53/C37 subcomplex of RNA polymerase III lies near the active site and participates in promoter opening

The C53 and C37 subunits of RNA polymerase III (pol III) form a subassembly that is required for efficient termination; pol III lacking this subcomplex displays increased processivity of RNA chain elongation. We show that the C53/C37 subcomplex additionally plays a role in formation of the initiation-ready open promoter complex similar to that of the Brf1 N-terminal zinc ribbon domain. In the absence of C53 and C37, the transcription bubble fails to stably propagate to and beyond the transcriptional start site even when the DNA template is supercoiled. The C53/C37 subcomplex also stimulates the formation of an artificially assembled elongation complex from its component DNA and RNA strands. Protein-RNA and protein-DNA photochemical cross-linking analysis places a segment of C53 close to the RNA 3' end and transcribed DNA strand at the catalytic center of the pol III elongation complex. We discuss the implications of these findings for the mechanism of transcriptional termination by pol III and propose a structural as well as functional correspondence between the C53/C37 subcomplex and the RNA polymerase II initiation factor TFIIF.

Poly(A) leader of eukaryotic mRNA bypasses the dependence of translation on initiation factors

Eukaryotic mRNAs in which a poly(A) sequence precedes the initiation codon are known to exhibit a significantly enhanced cap-independent translation, both in vivo and in cell-free translation systems. Consistent with high expression levels of poxviral mRNAs, they contain poly(A) sequences at their 5' ends, immediately before the initiation AUG codon. Here we show that poly(A) as a leader sequence in mRNA constructs promotes the recruitment of the 40S ribosomal subunits and the efficient formation of initiation complexes at cognate AUG initiation codons in the absence of two essential translation initiation factors, eIF3 and eIF4F. These factors are known to be indispensable for the cap-dependent (and ATP-dependent) mechanism of translation initiation but are shown here to be not required if an mRNA contains a 5'-proximal poly(A). Thus, the presence of a pre-AUG poly(A) sequence results in an alternative mechanism of translation initiation. It involves the binding of initiating 40S ribosomal subunits within the 5' UTR and their phaseless, ATP-independent, diffusional movement ("phaseless wandering") along the leader sequence, with subsequent recognition of the initiation (AUG) codon.

The role of an upstream promoter interaction in initiation of bacterial transcription

The bacterial RNA polymerase (RNAP) recognizes promoters through sequence-specific contacts of its promoter-specificity components (sigma) with two DNA sequence motifs. Contacts with the upstream ('-35') promoter motif are made by sigma domain 4 attached to the flap domain of the RNAP beta subunit. Bacteriophage T4 late promoters consist solely of an extended downstream ('-10') motif specifically recognized by the T4 gene 55 protein (gp55). Low level basal transcription is sustained by gp55-RNAP holoenzyme. The late transcription coactivator gp33 binds to the beta flap and represses this basal transcription. Gp33 can also repress transcription by Escherichia coli sigma70-RNAP holoenzyme mutated to allow gp33 access to the beta flap. We propose that repression is due to gp33 blocking an upstream sequence-independent DNA-binding site on RNAP (as sigma70 domain 4 does) but, unlike sigma70 domain 4, providing no new DNA interaction. We show that this upstream interaction is essential only at an early step of transcription initiation, and discuss the role of this interaction in promoter recognition and transcriptional regulation.

The bacteriophage T4 late-transcription coactivator gp33 binds the flap domain of Escherichia coli RNA polymerase

Transcription of bacteriophage T4 late genes requires concomitant DNA replication. T4 late promoters, which consist of a single 8-bp -10 motif, are recognized by a holoenzyme containing Escherichia coli RNA polymerase core and the T4-encoded promoter specificity subunit, gp55. Initiation of transcription at these promoters by gp55-holoenzyme is inefficient, but is greatly activated by the DNA-loaded DNA polymerase sliding clamp, gp45, and the coactivator, gp33. We report that gp33 attaches to the flap domain of the Escherichia coli RNA polymerase beta-subunit and that this interaction is essential for activation. The beta-flap also mediates recognition of -35 promoter motifs by binding to sigma(70) domain 4. The results suggest that gp33 is an analogue of sigma(70) domain 4 and that gp55 and gp33 together constitute two parts of the T4 late sigma. We propose a model for the role of the gp45 sliding clamp in activation of T4 late-gene transcription.

Reaction pathways in transcript elongation

Transcription of DNA into RNA is a central part of gene expression, and is highly regulated in all organisms. In order to approach transcription control systems on a molecular basis we must understand the mechanisms used by the transcription complex to discharge its various functions, which include transcript initiation, elongation, editing, and termination. In this article we describe recent progress in sorting out the multiple reaction pathways that are, at least in principle, available to the transcription complex at each DNA template position, and show how transcription control systems partition active complexes into these pathways. Understanding these regulatory processes requires an elucidation of the molecular details of how sequence- and factor-dependent changes in the conformations, stabilities, and reaction rates of the complexes determine function. Recent progress in unraveling these issues is summarized in this article and emerging principles that govern the regulation of the elongation phase of transcription are discussed.

An integrated model of the transcription complex in elongation, termination, and editing

Recent findings now allow the development of an integrated model of the thermodynamic, kinetic, and structural properties of the transcription complex in the elongation, termination, and editing phases of transcript formation. This model provides an operational framework for placing known facts and can be extended and modified to incorporate new advances. The most complete information about transcriptional mechanisms and their control continues to come from the Escherichia coli system, upon which most of the explicit descriptions provided here are based. The transcriptional machinery of higher organisms, despite its greater inherent complexity, appears to use many of the same general principles. Thus, the lessons of E. coli continue to be relevant.

The Nun protein of bacteriophage HK022 inhibits translocation of Escherichia coli RNA polymerase without abolishing its catalytic activities

Bacteriophage HK022 Nun protein blocks transcription elongation by Escherichia coli RNA polymerase in vitro without dissociating the transcription complex. Nun is active on complexes located at any template site tested. Ultimately, only the 3'-OH terminal nucleotide of the nascent transcript in an arrested complex can turn over; it is removed by pyrophosphate and restored with NTPs. This suggests that Nun inhibits the translocation of RNA polymerase without abolishing its catalytic activities. Unlike spontaneously arrested complexes, Nun-arrested complexes cannot be reactivated by transcription factor GreB. The various complexes show distinct patterns of nucleotide incorporation and pyrophosphorolysis before or after treatment with Nun, suggesting that the configuration of RNAP, transcript, and template DNA is different in each complex.

The COOH-terminal domain of the RNA polymerase alpha subunit in transcriptional enhancement and deactivation at the bacteriophage T4 late promoter

Many activator proteins generate their positive control of transcription through interactions with the COOH-terminal domain of the Escherichia coli RNA polymerase alpha subunit. We have examined the participation of this alpha-domain in transcriptional enhancement and suppression at bacteriophage T4 late promoters. Enhancement is generated by the T4 gene 45 protein, which is the DNA-tracking processivity factor of viral DNA replication; suppression of unenhanced transcription is generated by the RNA polymerase-binding co-activator T4 gene 33 protein. Enhanced and unenhanced transcription by RNA polymerase reconstituted with intact and truncated alpha subunits and by RNA polymerase containing ADP-ribosylated alpha has been compared; the internal structures of transcription complexes formed with these RNA polymerases have also been analyzed by footprinting and photocross-linking. Comparison of these structural and functional analyses suggests that enhancement of T4 late transcription by gp45 is not compatible with any significant role of the COOH-terminal domain of the RNA polymerase core alpha subunit in transcriptional initiation. Suppression of unenhanced T4 late transcription by the gene 33 protein also does not require the COOH-terminal domain of alpha.

Transcriptional activation by a DNA-tracking protein: structural consequences of enhancement at the T4 late promoter

Transcriptional initiation at bacteriophage T4 late promoters is activated from enhancer-like distal sites by the T4 gene 44, 62, and 45 DNA polymerase accessory proteins (gp44, gp62, and gp45, respectively). Enhancement is ATP hydrolysis-dependent and requires protein tracking along DNA. The structural analysis of the enhanced transcription initiation complex shows gp45 located at the upstream end of this promoter complex in the vicinity of its transcriptional coactivator, the T4 gene 33 protein. The ATP-cleaving gene 44 protein-gene 62 protein complex serves as the assembly factor for gp45, but does not stably associate with the enhanced promoter complex. Transcriptional enhancement quantitatively favors, but does not qualitatively change, DNA strand separation in the transcription bubble. A model of the transcriptional activation that rationalizes its DNA-tracking and activation-polarity properties is presented.

Phosphorolytic error correction during transcription

Escherichia coli DNA-directed RNA polymerase is shown to contain a novel phosphorolytic error correction activity which removes erroneous nucleotides, as rNDPs, from the 3'-end of the growing transcript. The activity we describe is biochemically similar to polynucleotide phosphorylase (PNP), yet in contrast to PNP is activated by Mn2+. We demonstrate that the activity, which is mediated by Pi, is dependent on the presence of an incorrectly incorporated nucleotide at the leading 3'-end of the transcript. The correction activity we describe exhibits a 4 x 10(4)-fold preference for the excision of incorrect nucleotides from the transcript. These findings suggest the possibility that RNA phosphorolysis may play a critical role in the process of transcriptional proofreading.

The DNA replication fork can pass RNA polymerase without displacing the nascent transcript

Replication proteins encoded by bacteriophage T4 generate DNA replication forks that can pass a molecule of Escherichia coli RNA polymerase moving in the same direction as the fork in vitro. The RNA polymerase ternary transcription complex remains bound to the DNA and retains a transcription bubble after the fork passes. The by-passed ternary complex can resume faithful RNA synthesis, suggesting that the multisubunit RNA polymerase of E. coli has evolved to retain its transcript after DNA replication, allowing partially completed transcripts to be elongated into full-length RNA molecules.

In vitro functional characterization of overproduced Escherichia coli katF/rpoS gene product

The katF/rpoS gene product (sigma s), a central regulator of stationary-phase gene expression in Escherichia coli, has been purified from an overproducing strain. sigma s was used as an immunogen for the production of monoclonal antibodies. Previous sequence analysis of sigma s strongly indicated homology to the sigma factor family. We show biochemically in this paper that sigma s is a sigma factor. This protein can bind to core RNA polymerase (E), and this binding can be competed effectively by the major E. coli transcription initiation factor, sigma 70. Immunopurified sigma s holoenzyme (E sigma s) transcribes the promoters of the bolAp1 gene and the xthA gene. Interestingly, both promoters can also be transcribed by sigma 70 holoenzyme (E sigma 70).

Lack of evidence for proofreading mechanisms associated with an RNA virus polymerase

The in vitro fidelity of the virion-associated RNA polymerase of vesicular stomatitis virus was quantitated for a single conserved viral RNA site and the usual high in vitro base misincorporation error frequencies (approx. 10(-3)) were observed at this (guanine) site. We sought evidence for RNA 3'-->5' exonuclease proofreading mechanisms by varying the concentrations of the next nucleoside triphosphate, by incorporation of nucleoside[1-thio]triphosphate analogues of the four natural RNA nucleosides, and by varying the concentrations of pyrophosphate in the in vitro polymerase reaction. None of these perturbations greatly affected viral RNA polymerase fidelity at the site studied. These results fail to show evidence for proofreading exonuclease activity associated with the virion replicase of an RNA virus. They suggest that RNA virus replication might generally be error-prone, because RNA replicase base misincorporations are proofread very inefficiently or not at all.

Mutational analysis of the bacteriophage P1 late promoter sequence Ps

The bacteriophage P1 late promoter sequence Ps controls the expression of the genes in the tail-fibre operon. Transcription from Ps only occurs during the second half of the P1 vegetative growth cycle and is positively regulated by the product of the phage gene 10. In this study degenerate oligonucleotides were used as primers in site-directed mutagenesis reactions in order to construct a large set of point mutations within the late promoter sequence Ps. A total of 35 independent single point mutations was isolated and the mutants were tested for promoter activity. Mutations in the Escherichia coli-like -10 region and in a late operator sequence, containing a symmetric sequence centred around position -22, resulted in significant reductions in promoter strength. Most of these mutations alter base-pairs that are highly conserved among the known late promoter sequences of the P1 family. In addition, insertion mutants that change the spacing between the -10 and the late operator indicate that a special topological arrangement between the two boxes is crucial for late promoter function. These results suggest that the product of gene 10 binds specifically to a late operator in order to activate transcription from P1 late promoter sequences.

A transcriptional enhancer whose function imposes a requirement that proteins track along DNA

Transcriptional regulation of the bacteriophage T4 late genes requires the participation of three DNA polymerase accessory proteins that are encoded by T4 genes 44, 62, and 45, and that act at an enhancer-like site. Transcriptional activation by these DNA replication proteins also requires the function of an RNA polymerase-bound coactivator protein that is encoded by T4 gene 33 and a promoter recognition protein that is encoded by T4 gene 55. Transcriptional activation in DNA constructs, in which the enhancer and a T4 late promoter can be segregated on two rings of a DNA catenane, has now been analyzed. The ability of an interposed DNA-binding protein to affect communication between the enhancer and the promoter was also examined. Together, these experiments demonstrate that this transcription-activating signal is conveyed between its enhancer and a T4 late promoter by a DNA-tracking mechanism. Alternative activation mechanisms relying entirely on through-space interactions of enhancer-bound and promoter-bound proteins are excluded.

Gene rIII is the nearest downstream neighbour of bacteriophage T4 gene 31

The nucleotide sequence of the 2218-bp T4 DNA fragment encompassing gene 31 and five complete open reading frames (ORFs) is presented. We show here that one of these ORFs, ORF31.-1, located downstream from gene 31, is the rIII gene. The position of the gene was established by comparison with the sequences of the rIII gene mutants, r67, rES40 and rBB9. The ORF corresponding to the rIII gene encodes a basic protein of 82 amino acids with an M(r) of 9323 and a pI of 9.28. According to the Chou and Fasman [Adv. Enzymol. 47 (1978) 45-148] secondary structure prediction, the rIII protein has a relatively high helical content. In addition, discrepancies with the overlapping sequences determined by other authors in this region are indicated.

An internal AUU codon initiates a smaller peptide encoded by bacteriophage T4 baseplate gene 26

Bacteriophage T4 baseplate gene 26 codes for two in-frame overlapping peptides with identical C-terminal regions. By site-directed mutagenesis we have now determined that an internal AUU, codon 114 of gene 26, is used as the initiation codon for the synthesis of a smaller peptide (gp26*). Thus gene 26* gives rise to a peptide of 95 amino acid residues with an Mr of 10,873, while the complete gene 26 encodes a peptide of 208 amino acid residues of M(r) 23,880. Expression of gene 26* is shown to depend on the RNA secondary structure in the translational initiation region of this gene.

A freeze-frame view of eukaryotic transcription during elongation and capping of nascent mRNA

Ribonuclease footprinting of nascent messenger RNA within ternary complexes of vaccinia RNA polymerase revealed an RNA binding site that encompasses an 18-nucleotide RNA segment. The dimensions of the binding site did not change as the polymerase moved along the template. Capping of the 5' end of the RNA was cotranscriptional and was confined to nascent chains 31 nucleotides or greater in length. Purified capping enzyme formed a binary complex with RNA polymerase in solution in the absence of nucleic acid. These findings suggest a mechanism for cotranscriptional establishment of messenger RNA identity in eukaryotes.

RNA virus populations as quasispecies

RNA virus mutation frequencies generally approach maximum tolerable levels, and create complex indeterminate quasispecies populations in infected hosts. This usually favors extreme rates of evolution, although periods of relative stasis or equilibrium, punctuated by rapid change may also occur (as for other life forms). Because complex quasispecies populations of RNA viruses arise probabilistically and differentially in every host, their compositions and exact roles in disease pathogenesis are indeterminate and their directions of evolution, and the nature and timing of "new" virus outbreaks are unpredictable.

Bacteriophage P1 gene 10 encodes a trans-activating factor required for late gene expression

Amber mutants of bacteriophage P1 were used to identify functions involved in late regulation of the P1 lytic growth cycle. A single function has been genetically identified to be involved in activation of the phage-specific late promoter sequence Ps. In vivo, P1 gene 10 amber mutants fail to trans activate a lacZ operon fusion under the transcriptional control of promoter Ps. Several P1 segments, mapping around position 95 on the P1 chromosome, were cloned into multicopy plasmid vectors. Some of the cloned DNA segments had a deleterious effect on host cells unless they were propagated in a P1 lysogenic background. By deletion and sequence analysis, the harmful effect could be delimited to a 869-bp P1 fragment, containing a 453-bp open reading frame. This open reading frame was shown to be gene 10 by sequencing the amber mutation am10.1 and by marker rescue experiments with a number of other gene 10 amber mutants. Gene 10 codes for an 18.1-kDa protein showing an unusually high density of charged amino acid residues. No significant homology to sequences present in the EMBL/GenBank data base was found, and the protein contained none of the currently known DNA-binding motifs. An in vivo trans activation assay system, consisting of gene 10 under the transcriptional control of an inducible promoter and a gene S/lacZ fusion transcribed from Ps, was used to show that gene 10 is the only phage-encoded function required for late promoter activation.

Bacteriophage SPO1 middle transcripts

Phage SPO1 middle transcripts are known to fall into two classes, m and m1l. Class m1l transcripts continue to be made late in the viral infection, while the synthesis of class m transcripts ceases soon after the onset of replication and late transcription. The experiments that are reported here deal with the regulatory nature of this diversity. The accumulation of transcripts associated with eight middle promoters was analyzed by S1 nuclease mapping. DNA sequence surrounding these middle promoters was determined or redetermined, and the stability of RNA associated with most of these promoters was also analyzed. Class m1l transcription was shown to be associated with SPO1 middle promoters that remain active at late stages of viral development, when middle promoters of class m are repressed. The consensus sequences of class m and m1l middle promoters were found to be indistinguishable and the search for sequences consensual with late promoters yielded only divergent candidates. No other consensus sequence that is specific and exclusive to either class of middle promoters was detected within a hundred base pairs upstream or downstream of these promoters. Considerable variations in the stabilities of SPO1 middle transcripts were found. Two promoters that are only 71 base pairs apart yielded transcripts that had substantially different stabilities. The 5'-flanking segment of the transcript associated with the upstream promoter apparently conferred a high degree of stability on this RNA.

Messenger RNA editing and the genetic code

Messenger RNA editing is defined as a process leading to predetermined modifications of the coding region of a primary gene transcript. By this definition, splicing processes are special forms of editing; however, they are not dealt with in this review. Editing processes different from splicing have been defined in mammalian cells, in RNA viruses, and in mitochondria of trypanosomes, higher plants and vertebrates. These post- or co-transcriptional processes involve addition, deletion, or modification-substitution of nucleotides, and represent previously unrecognized mechanisms for altering the coding potential of a gene and for modulating gene expression.

Heterogeneous initiation due to slippage at the bacteriophage 82 late gene promoter in vitro

RNAs synthesized in vitro by purified Escherichia coli RNA polymerase from a bacteriophage 82 promoter are heterogeneous at the 5' end. We show that this heterogeneity results from variable addition of extra adenine residues, allowed by slippage of the initial oligonucleotide pppAAA-OH against its DNA template sequence TTT. Slippage backward by one base allows another A to be added, giving pppAAAA-OH, and this cycle can continue more than 20 times before it is ended by incorporation of UMP encoded by the fourth template base A. Slippage is abolished by mutation of the TTT template sequence to TGT and is sensitive to the concentrations of UTP and ATP in the reaction mixture. Analysis of deletions, substitutions, and point mutants implies that the slippage reaction requires only the existence of TTT at the initiation site of the template strand, although changes in neighboring nucleotides slightly affect its efficiency.

Thermodynamic analysis of the transcription cycle in E. coli

The E. coli RNA transcription cycle can be divided into three major phases, which are generally called initiation, elongation, and termination. In this paper, we review recent biophysical studies of the interactions of the transcriptional regulatory proteins, sigma 70 and NusA, with themselves and with core RNA polymerase in solution, as well as with core polymerase within the transcription complex. The different affinities of sigma 70 and NusA for core RNA polymerase at various stages in the transcription cycle, together with other quantitative data, are then used to construct a partial free energy diagram for the overall transcription process. This thermodynamic framework, which is interrupted by at least two irreversible steps, can be used to rationalize physiological aspects of the transcription cycle and its regulation, as well as to identify crucial points at which our knowledge is still incomplete.

RNA chain elongation by Escherichia coli RNA polymerase. Factors affecting the stability of elongating ternary complexes

We have devised a method to follow the stability of individual ternary transcription complexes containing Escherichia coli RNA polymerase halted at many different sites along a DNA template during the transcription process. Studies of complexes formed with phage T7 DNA templates reveal at least three general classes of ternary complexes that differ dramatically in their properties. Complexes of one sort (normal complexes) are highly stable to dissociation and denaturation under a variety of solution conditions. They remain intact and active for up to 24 hours even in salt concentrations up to 1 M-K+. This suggests that they are stabilized to a significant extent by non-ionic interactions between RNA polymerase and the nucleic acids. We consider these to be the normal complexes formed during RNA chain elongation. Complexes of a second sort (release complexes) dissociate rapidly, releasing free RNA transcripts and active RNA polymerase. The rate of dissociation is substantially enhanced by elevated concentrations of K+, hence the interaction between RNA polymerase and nucleic acids in these complexes is stabilized predominantly by ionic interactions. However, release complexes are stabilized by millimolar concentrations of Mg2+, which as been implicated in stabilization of the binding of RNA to free RNA polymerase. These complexes are formed at DNA sequences that we refer to as release sites. Analysis of DNA sequences at release sites reveals that all share a common feature, the potential to form an RNA hairpin in the region just upstream from the actual 3' end of the released RNA. Experiments incorporating IMP in the transcript and blocking potential hairpin formation with DNA oligomers support a direct role for an RNA hairpin in triggering the release reaction. Changes in the 3'-proximal DNA sequences generally have little effect on the presence or rate of the release reaction, although there are significant exceptions. The results suggest that the presence of certain RNA hairpins in the region six to ten nucleotides upstream from the transcript growing point can trigger a substantial structural transition in the ternary transcription complex, forming a "release mode" complex from which transcript dissociation is facilitated. This release, mode complex may be a central intermediate in RNA chain termination. A final class of complexes (dead-end complexes) appear to be elongating complexes that have entered a state or conformation that is stable, but is blocked in resuming the normal elongation reaction. Such complexes bear active RNA polymerase, and can be restarted after limited pyrophosphorolysis. The structural elements that determine the formation of dead-end complexes are not yet known.

S. cerevisiae TFIIIB is the transcription initiation factor proper of RNA polymerase III, while TFIIIA and TFIIIC are assembly factors

The S. cerevisiae RNA polymerase III (pol III) transcription factor TFIIIB binds to DNA upstream of the transcription start site of the SUP4 tRNA(Tyr) gene in a TFIIIC-dependent reaction and to the major 5S rRNA gene in a reaction requiring TFIIIC and TFIIIA. It is shown here that TFIIIB alone correctly positions pol III for repeated cycles of transcription on both genes, with the same efficiency as fully assembled transcription complexes. Thus, TFIIIB is the sole transcription initiation factor of S. cerevisiae pol III; TFIIIC and TFIIIA are assembly factors for TFIIIB. The TFIIIB-dependent binding of pol III to the SUP4 tRNA and 5S rRNA genes has been analyzed in binary (protein and DNA only) and precisely arrested ternary (protein, DNA, and RNA) transcription complexes. Pol III unwinds at least 14 bp of DNA at the SUP4 transcription start in a temperature-dependent process. The unwound DNA segment moves downstream with nascent RNA as a transcription bubble of approximately the same size.

Structure of vaccinia virus late promoters

Functional elements of vaccinia virus late promoters were characterized by mutagenesis. Synthetic oligonucleotides were inserted into a plasmid vector containing the lacZ gene of Escherichia coli flanked by sequences from the thymidine kinase (TK) gene of vaccinia virus. The lacZ gene, under control of the synthetic promoter, was introduced into the vaccinia virus genome at the TK locus by homologous recombination, and each of the 122 recombinants thus obtained was assayed for beta-galactosidase expression. The relative amounts and 5' ends of lacZ mRNAs specified by a subset of the recombinants were determined by primer extension. The analysis indicated that late promoters may be considered in terms of three regions; an upstream sequence of about 20 base-pairs, rich in T and A residues, separated by a spacer region of about six base-pairs from a highly conserved (-1)TAAAT(+4) element within which transcription initiates. All single nucleotide substitutions within the three A residues of the TAAAT, as well as the addition of a fourth A residue, caused drastic reductions in promoter strength. All substitutions of the T residues at -1 and +4 were also detrimental to promoter activity, to an extent that depended on the strength of the promoter as determined by the upstream sequence. mRNA synthesis appeared to initiate within the three A residues regardless of promoter strength. The 5'-poly(A) leader, which is a unique feature of poxvirus late mRNAs, was diminished in length when either of the T residues at -1 and +4 was mutated, was absent or limited to a few nucleotides when any of the three A residues was substituted, but was unaffected by changes outside the TAAAT sequence. The data are consistent with a model for the generation of the normal 5'-poly(A) leader by an RNA polymerase slippage mechanism requiring three consecutive A residues. Single nucleotide substitutions within the six base-pairs upstream and three base-pairs downstream from the TAAAT sequence had modest effects on promoter strength. The most and least favourable changes led to a fourfold increase and an eightfold decrease in activity, respectively. Sequences further upstream were essential for late promoter function; tracts of T or A residues enhanced expression up to 20-fold, the former conferring much greater activity. Highest expression was obtained with a tract of 18 or 20 T residues.(ABSTRACT TRUNCATED AT 400 WORDS)

RNA chain initiation by Escherichia coli RNA polymerase. Structural transitions of the enzyme in early ternary complexes

We have studied the properties and structures of a series of Escherichia coli RNA polymerase ternary complexes formed during the initial steps of RNA chain initiation and elongation. Five different templates were used that contained the bacteriophage T7 A1 promoter or the E. coli Tac or the lac UV5 promoter, as well as variant templates with alterations in the initial transcribed regions. The majority of ternary complexes bearing short transcripts (from two to nine nucleotides) are highly unstable and cannot be easily studied. This includes transcripts from the phage T7 A1 promoter, for which the stability of complexes bearing transcripts as short as four nucleotides has previously been postulated. However, with one Tac promoter template, RNA polymerase forms ternary complexes with transcripts as short as five nucleotides that are stable enough for biochemical study. We describe several approaches to identifying and isolating such stable complexes and show that stringent criteria are needed in carrying out such experiments if the results are to be meaningful. Deoxyribonuclease I (DNase I) footprinting has been used to probe the general structure of the stable ternary complexes formed as the polymerase begins transcription and moves away from the start site. The enzyme undergoes a sequence of structural changes during initiation and transition to an elongating complex. Complexes with five to eight nucleotide transcripts, designated initial transcribing complexes (ITC), have identical footprints; they all retain the sigma factor and have a slightly extended DNase I footprint (-57 to +24) as compared to the open promoter complex (-57 to +20). ITC complexes all show a region of marked DNase I hypersensitivity in the -25 region that may reflect bending or distortion of the DNA template. Complexes with 10 or 11 nucleotide transcripts, designated initial elongating complexes (IEC), have lost the sigma factor and have a slightly reduced and shifted DNase I footprint (-32 to +30). However, these IEC have not yet achieved the much smaller footprint (approximately 30 bp) reported as characteristic of elongating ternary complexes bearing longer RNA chains. During the initial phase of transcription, the RNA polymerase does not move monotonically along the DNA template as RNA chains are extended, but instead, the upstream and downstream contacts remain more or less fixed as the nascent transcript is elongated up to about eight nucleotides in length. Only after incorporation of 10 nucleotides is there significant movement of the enzyme away from the promoter region and a commitment to elongation.

Enhancement of bacteriophage T4 late transcription by components of the T4 DNA replication apparatus

The expression of the late genes in bacteriophage T4 development is closely connected to viral DNA replication. Three T4-encoded DNA polymerase accessory proteins are shown to stimulate transcription at T4 late promoters in an adenosine triphosphate (ATP) hydrolysis-requiring process. The properties of the activation resemble those found for enhancers of eukaryotic transcription. However, the nature of the enhancer of T4 late transcription is novel in that it is a structure--a break in the nontranscribed DNA stand--to which the three replication proteins bind, rather than a sequence. Since the three DNA polymerase accessory proteins are carried on the moving replication fork as part of the replisome, we postulate that viral DNA replication forks act, in vivo, as the mobile enhancers of T4 late gene transcription. Whereas Escherichia coli RNA polymerase bearing the T4 gene 55 protein can selectively recognize T4 late promoters, it is only capable of responding to the transcription-enhancing activity of the three replication proteins on acquiring an additional T4-specific modification.

Bacteriophage T4 late gene expression: overlapping promoters direct divergent transcription of the base plate gene cluster

Eight 5' ends of RNA molecules which encompass the bacteriophage T4 base plate late genes 51 to 26 region have been mapped by S1 nuclease protection and reverse transcription within a 246-bp DNA segment. Two of eight 5' ends are initiated at two absolutely conserved late promoter sites, P51 and P26a, that direct RNA synthesis on opposite strands. These two promoters share four of eight promoter sequence base pairs. A third 5' end arises from another promoter, P26b, which shows one base pair mismatch with respect to the absolutely conserved -10 sequence. All the other 5' ends arise from RNA processing and/or degradation. Since no other late transcription promoter sites were found within the base plate cluster sequence, we propose that the two overlapping late promoters, P51 and P26a, direct the expression of the T4 base plate gene cluster, included between map coordinates 114,000 and 121,038: P51 directs the transcription of genes 51, 27, 28, 29, 48, and 54 on the rDNA strand and P26a the transcription of genes 26 and 25 on the /DNA strand. This peculiar promoter configuration might account for the low level of transcription of these late genes.

Reversibility of nucleotide incorporation by Escherichia coli RNA polymerase, and its effect on fidelity

During transcription, Escherichia coli RNA polymerase is capable of removing the nucleotide that it has just added to a growing RNA chain, and this removal depends on the presence of small concentrations of pyrophosphate. Chemically, the removal reaction is simply the reversal of the incorporation reaction, and we have observed the generation of free triphosphate as a result. After the removal the enzyme can continue synthesis. To test whether this reaction can provide an error correction mechanism, misincorporation rates were measured at a single position in an RNA transcript by withholding the correct nucleotide for that position, measuring the amount of readthrough transcript, and analyzing the readthrough transcripts with nearest-neighbor analysis and enzymatic RNA sequencing. The removal of pyrophosphate increases the rate of misincorporation. We present a theory that explains how reversible incorporation can increase the available discrimination free energy between correct and incorrect nucleotides and therefore may increase the fidelity of transcription. The formation of a covalent phosphodiester bond allows discrimination on the basis of helical structure as well as base-pairing. We propose that the important discrimination step is the translocation of the enzyme from one site on the DNA template to the next, and that reversible incorporation is necessary in order to take full advantage of the maximum discrimination free energy.

Chromosomal loop/nuclear matrix organization of transcriptionally active and inactive RNA polymerases in HeLa nuclei

The relative distribution of transcriptionally active and inactive RNA polymerases I and II between the nuclear matrix/scaffold and chromosomal loops of HeLa cells was determined. Total RNA polymerase was assessed by immunoblotting and transcribing RNA polymerase by a photoaffinity labeling technique in isolated nuclei. Nuclear matrix/scaffold was isolated by three methods using high-salt, intermediate-salt or low-salt extraction. The distribution of RNA polymerases I and II were very similar within each of the methods, but considerable differences in distributions were found between the different preparation methods. Either intermediate-salt or high-salt treatment of DNase I-digested nuclei showed significant association of RNA polymerases with the nuclear matrix. However, intermediate-salt followed by high-salt treatment released all transcribing and non-transcribing RNA polymerases. Nuclear scaffolds isolated with lithium diiodosalicylate (low-salt) contained very little of the RNA polymerases. This treatment, however, caused the dissociation of RNA polymerase II transcription complexes. These results show unambiguously that RNA polymerases, both in their active and inactive forms, are not nuclear matrix proteins. The data support models in which the transcriptional machinery moves around DNA loops during transcription.

The structure of three bacteriophage T4 genes required for tail-tube assembly

Three different protein molecules copurify with T4 tail tubes after the tubes are released from the baseplate by guanidine hydrochloride treatment. These tube-associated proteins (TAPs) are the products of genes 29, 48, and 54. To further investigate the structural roles that these proteins may play in T4 tail assembly we have cloned and sequenced the genes coding for these proteins and have deduced their predicted amino acid sequences. The sequence data reveal a region of amino acid sequence similarity between gp54 and the T4 tail-tube structural protein, gp19. We believe that this region of similarity is significant and consistent with the role gp54 may play in initiating T4 tail-tube polymerization.

Isolation and properties of transcribing ternary complexes of Escherichia coli RNA polymerase positioned at a single template base

We have studied the conditions needed for the formation of stable ternary complexes by Escherichia coli RNA polymerase using a procedure in which elongation by the majority of active enzyme molecules is halted at a specific template base. Stable complexes of this sort, containing RNA chains as short as 15 nucleotides, have been formed from three different promoter sites (T7 A1, lambda PL, and E. coli rrnB P1) using di- and trinucleotides as primers in reactions limited by the presence of only three of the nucleoside triphosphate substrates. The resulting ternary complexes can be stored for at least five days without loss in activity, and provide useful reagents and substrates for studies of the properties of RNA polymerases engaged in chain elongation and termination. At all three promoter sites abortive initiation, leading to synthesis and release of oligomers up to ten nucleotides, competes with productive initiation, leading to the formation of stable elongating complexes. Thus the relative instability of ternary RNA polymerase complexes bearing transcripts shorter than ten nucleotides may be a general feature of the transcription initiation reaction.