Bacteriophage T4 early promoter regions. Consensus sequences of promoters and ribosome-binding sites

The evolution of a counter-defense mechanism in a virus constrains its host range

Bacteria use diverse immunity mechanisms to defend themselves against their viral predators, bacteriophages. In turn, phages can acquire counter-defense systems, but it remains unclear how such mechanisms arise and what factors constrain viral evolution. Here, we experimentally evolved T4 phage to overcome a phage-defensive toxin-antitoxin system, toxIN, in E. coli. Through recombination, T4 rapidly acquires segmental amplifications of a previously uncharacterized gene, now named tifA, encoding an inhibitor of the toxin, ToxN. These amplifications subsequently drive large deletions elsewhere in T4's genome to maintain a genome size compatible with capsid packaging. The deleted regions include accessory genes that help T4 overcome defense systems in alternative hosts. Thus, our results reveal a trade-off in viral evolution; the emergence of one counter-defense mechanism can lead to loss of other such mechanisms, thereby constraining host range. We propose that the accessory genomes of viruses reflect the integrated evolutionary history of the hosts they infected.

Characterization of a ViI-like phage specific to Escherichia coli O157:H7

Phage vB_EcoM_CBA120 (CBA120), isolated against Escherichia coli O157:H7 from a cattle feedlot, is morphologically very similar to the classic phage ViI of Salmonella enterica serovar Typhi. Until recently, little was known genetically or physiologically about the ViI-like phages, and none targeting E. coli have been described in the literature. The genome of CBA120 has been fully sequenced and is highly similar to those of both ViI and the Shigella phage AG3. The core set of structural and replication-related proteins of CBA120 are homologous to those from T-even phages, but generally are more closely related to those from T4-like phages of Vibrio, Aeromonas and cyanobacteria than those of the Enterobacteriaceae. The baseplate and method of adhesion to the host are, however, very different from those of either T4 or the cyanophages. None of the outer baseplate proteins are conserved. Instead of T4's long and short tail fibers, CBA120, like ViI, encodes tail spikes related to those normally seen on podoviruses. The 158 kb genome, like that of T4, is circularly permuted and terminally redundant, but unlike T4 CBA120 does not substitute hmdCyt for cytosine in its DNA. However, in contrast to other coliphages, CBA120 and related coliphages we have isolated cannot incorporate 3H-thymidine (3H-dThd) into their DNA. Protein sequence comparisons cluster the putative "thymidylate synthase" of CBA120, ViI and AG3 much more closely with those of Delftia phage φW-14, Bacillus subtilis phage SPO1, and Pseudomonas phage YuA, all known to produce and incorporate hydroxymethyluracil (hmdUra).

Multiple controls regulate the expression of mobE, an HNH homing endonuclease gene embedded within a ribonucleotide reductase gene of phage Aeh1

Mobile genetic elements have the potential to influence the expression of genes surrounding their insertion site upon invasion of a genome. Here, we examine the transcriptional organization of a ribonucleotide reductase operon (nrd) that has been invaded by an HNH family homing endonuclease, mobE. In Aeromonas hydrophila phage Aeh1, mobE has inserted into the large-subunit gene (nrdA) of aerobic ribonucleotide reductase (RNR), splitting it into two smaller genes, nrdA-a and nrdA-b. This gene organization differs from that in phages T4, T6, RB2, RB3, RB15, and LZ7, where mobE is inserted in the nrdA-nrdB intergenic region. We present evidence that the expression of Aeh1 mobE is regulated by transcriptional, posttranscriptional, and translational controls. An Aeh1-specific late promoter drives expression of mobE, but strikingly the mobE transcript is processed internally at an RNase E-like site. We also identified a putative stem-loop structure upstream of mobE that sequesters the mobE ribosome binding site, presumably acting to down regulate MobE translation. Moreover, our transcriptional analyses indicate that the surrounding nrd genes of phage Aeh1 are expressed by a different strategy than are the corresponding phage T4 genes and that transcriptional readthrough is the only mechanism by which the promoterless Aeh1 nrdB gene is expressed. We suggest that the occurrence of multiple layers of control to limit the expression of mobE to late in the Aeh1 infection cycle is an adaptation of Aeh1 to reduce any effects on expression of the surrounding nrd genes early in phage infection when RNR function is critical.

Middle promoters constitute the most abundant and diverse class of promoters in bacteriophage T4

The temporally regulated transcription program of bacteriophage T4 relies upon the sequential utilization of three classes of promoters: early, middle and late. Here we show that middle promoters constitute perhaps the largest and the most diverse class of T4 promoters. In addition to 45 T4 middle promoters known to date, we mapped 13 new promoters, 10 of which deviate from the consensus MotA box, with some of them having no obvious match to it. So, 30 promoters of 58 identified now deviate from the consensus sequence deduced previously. In spite of the differences in their sequences, the in vivo activities of these T4 middle promoters were demonstrated to be dependent on both activators, MotA and AsiA. Traditionally, the MotA box was restricted to a 9 bp sequence with the highly conserved motif TGCTT. New logo based on the sequences of currently known middle promoters supports the conclusion that the consensus MotA box is comprised of 10 bp with the highly conserved central motif GCT. However, some apparently good matches to the consensus of middle promoters do not produce transcripts either in vivo or in vitro, indicating that the consensus sequence alone does not fully define a middle promoter.

Electrostatic properties of promoter recognized by E. coli RNA polymerase Esigma70

A comparative analysis of electrostatic patterns for 359 sigma70-specific promoters and 359 nonpromoter regions on electrostatic map of Escherichia coli genome was carried out. It was found that DNA is not a uniformly charged molecule. There are some local inhomogeneities in its electrostatic profile which correlate with promoter sequences. Electrostatic patterns of promoter DNAs can be specified due to the presence of some distinctive motifs which differ for different promoter groups and may be involved as signal elements in differential recognition of various promoters by the enzyme. Some specific electrostatic elements which are responsible for modulating promoter activities due to ADP-ribosylation of RNA polymerase alpha-subunit were found in far upstream regions of T4 phage early promoters and E. coli ribosomal promoters.

Transcription and RNA processing during expression of genes preceding DNA ligase gene 30 in T4-related bacteriophages

Early gene expression in bacteriophage T4 is controlled primarily by the unique early promoters, while T4-encoded RegB endoribonuclease promotes degradation of many early messages contributing to the rapid shift of gene expression from the early to middle stages. The regulatory region for the genes clustered upstream of DNA ligase gene 30 of T4 was known to carry two strong early promoters and two putative RegB sites. Here, we present the comparative analysis of the regulatory events in this region of 16 T4-type bacteriophages. The regulatory elements for control of this gene cluster, such as rho-independent terminator, at least one early promoter, the sequence for stem-loop structure, and the RegB cleavage sites have been found to be conserved in the phages studied. Also, we present experimental evidence that the initial cleavage by RegB of phages TuIa and RB69 enables degradation of early phage mRNAs by the major Escherichia coli endoribonuclease, RNase E.

Phage T4 early promoters are resistant to inhibition by the anti-sigma factor AsiA

Phage T4 early promoters are transcribed in vivo and in vitro by the Escherichia coli RNA polymerase holoenzyme Esigma(70). We studied in vitro the effects of the T4 anti-sigma(70) factor AsiA on the activity of several T4 early promoters. In single-round transcription, promoters motB, denV, mrh.2, motA wild type and UP element-deleted motA are strongly resistant to inhibition by AsiA. The alpha-C-terminal domain of Esigma(70) is crucial to this resistance. DNase I footprinting of Esigma(70) and Esigma(70)AsiA on motA and mrh.2 shows extended contacts between the holoenzyme with or without AsiA and upstream regions of these promoters. A TG --> TC mutation of the extended -10 motif in the motA UP element-deleted promoter strongly increases susceptibility to inhibition by AsiA, but has no effect on the motA wild-type promoter: either the UP element or the extended -10 site confers resistance to AsiA. Potassium permanganate reactivity shows that the two structure elements are not equivalent: with AsiA, the motA UP element-deleted promoter opens more slowly whereas the motA TC promoter opens like the wild type. Changes in UV laser photoreactivity at position +4 on variants of motA reveal an analogous distinction in the roles of the extended -10 and UP promoter elements.

The sequences and activities of RegB endoribonucleases of T4-related bacteriophages

The RegB endoribonuclease encoded by bacteriophage T4 is a unique sequence-specific nuclease that cleaves in the middle of GGAG or, in a few cases, GGAU tetranucleotides, preferentially those found in the Shine-Dalgarno regions of early phage mRNAs. In this study, we examined the primary structures and functional properties of RegB ribonucleases encoded by T4-related bacteriophages. We show that all but one of 36 phages tested harbor the regB gene homologues and the similar signals for transcriptional and post-transcriptional autogenous regulation of regB expression. Phage RB49 in addition to gpRegB utilizes Escherichia coli endoribonuclease E for the degradation of its transcripts for gene regB. The deduced primary structure of RegB proteins of 32 phages studied is almost identical to that of T4, while the sequences of RegB encoded by phages RB69, TuIa and RB49 show substantial divergence from their T4 counterpart. Functional studies using plasmid-phage systems indicate that RegB nucleases of phages T4, RB69, TuIa and RB49 exhibit different activity towards GGAG and GGAU motifs in the specific locations. We expect that the availability of the different phylogenetic variants of RegB may help to localize the amino acid determinants that contribute to the specificity and cleavage efficiency of this processing enzyme.

Twelve new MotA-dependent middle promoters of bacteriophage T4: consensus sequence revised

Bacteriophage T4 middle-mode transcription requires Escherichia coli RNA polymerase, phage-encoded transcriptional activator MotA and co-activator AsiA that form a complex at a middle promoter DNA. T4 middle promoters have been defined by a consensus sequence deduced from the list of 14 middle promoters identified in earlier studies. To date, 33 middle promoters have been mapped on the T4 genome. Of these, 12 contain differences even at the highly conserved positions of the consensus sequence. In the T4 prereplicative gene cluster between genes e and rpbA, we have identified 12 new middle promoters, most of which contain differences from the consensus sequence deduced previously. Analysis of base conservation in the different sequence positions of new middle promoters, as well as those identified previously, revealed some new features of middle T4 promoters. We propose to define these promoters by a MotA box (a/t)(a/t)(a/t)TGCTTtA centred at the position -30, the sequence TAtaAT centred at -10 relative to the transcriptional start site, and the spacer region of 12(+/-1) base-pairs between them.

Bacteriophage T4 genome

Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene products. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods. The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition. Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level. The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments. Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the "cell-puncturing device," combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection. Despite these advances, nearly 130 potential T4 genes remain uncharacterized. Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli. T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex evolution and ecology of phages-the most abundant and among the most ancient biological entities on Earth.

Identification of two middle promoters upstream DNA ligase gene 30 of bacteriophage T4

Bacteriophage T4 DNA ligase gene 30 lies in the cluster of prereplicative genes located counterclockwise from map units 149 to 121. Based on the early transcription studies this gene has been considered as a typical early gene of bacteriophage T4. In agreement with this assignment, two strong T4 early promoters, P(E )30.8 (128.6) and P(E )30.7 (128.2), located about 3.1 and 2.7 kb upstream from gene 30 have been revealed by promoter mapping and sequence analysis. In addition, the existence of a putative early promoter just upstream of gene 30 was proposed from the sequence data. However, here we show that the putative early promoter just upstream of gene 30 is, in fact, a T4 middle promoter. Furthermore, we detected one more middle promoter located in the genomic region between early promoter P(E )30.7 (128.2) and DNA ligase gene 30 in the coding region of gene 30.3. Both new middle promoters have differences from the consensus MotA box, while their -10 regions match the sigma(70) consensus sequence very well. The 5' ends of MotA-dependent transcripts directed from these promoters, as well as the kinetics of 5' end accumulation in the cells, have been determined by primer extension analysis. The results of these analyses indicate that both MotA-dependent and MotA-independent promoters control the transcription of T4 DNA ligase gene 30 in vivo. Moreover, we show that the first transcripts for gene 30 are directed from its own middle promoter, P(M)30.

Cloning, sequencing, expression and promoter analysis of a structural protein of bacteriophage MB78

Bacteriophage MB78, a virulent phage of Salmonella typhimurium isolated in our laboratory. It is different from the well-known temperate phage P22 and 9NA. A detailed physical map has been constructed. To understand more about the physiology and genetics of this interesting phage it has become necessary to fragment the phage genome, clone the fragments and analyze in depth. A number of promoters of bacteriophage MB78 have been cloned and characterized recently. As a part of this program, in this investigation, we report cloning, sequencing and expression and promoter analysis of the ClaI G fragment. We identified the expressed protein as phage structural. Phage structural proteins play a vital role in forming the core head of the phage particle.

RNA polymerase--promoter recognition. Specific features of electrostatic potential of "early" T4 phage DNA promoters

Comparative analysis of electrostatic potential distribution for "early" T4 phage promoters was undertaken, along with calculation of topography of electrostatic potential around the native and ADP-ribosylated C-terminal domain of RNA polymerase alpha-subunit. The data obtained indicate that there is specific difference in the patterns of electrostatic potential distribution in far upstream regions of T4 promoters differing by their response to ADP-ribosylation of RNA polymerase. A specific change in profiles of electrostatic potential distribution for the native and ADP-ribosylated forms of RNA polymerase alpha-subunit was observed suggesting that this factor may be responsible for modulating T4 promoter activities in response to the enzyme modification.

T4 early promoter strength probed in vivo with unribosylated and ADP-ribosylated Escherichia coli RNA polymerase: a mutation analysis

The consensus sequence of T4 early promoters differs in length, sequence and degree of conservation from that of Escherichia coli sigma(70) promoters. The enzyme interacting with these promoters, and transcribing the T4 genome, is native host RNA polymerase, which is increasingly modified by the phage-encoded ADP-ribosyltransferase, Alt. T4 early transcription is a very active process, possibly out-competing host transcription. The much stronger T4 promoters enhance viral transcription by a factor of at least two and the Alt-catalysed ADP-ribosylation of the host enzyme triggers an additional enhancement, again by a factor of about two. To address the question of which promoter elements contribute to the increasing transcriptional activity directed towards phage genes, the very strong E. coli promoter, Ptac, was sequentially mutated towards the sequence of the T4 early promoter consensus. Second, mutations were introduced into the highly conserved regions of the T4 early promoter, P8.1. The co-occurrence of the promoter-encoding plasmid pKWIII and vector pTKRI, which expresses Alt in E. coli, constitutes a test system that allows comparison of the transcriptional activities of phage and bacterial promoters, in the presence of native, or alternatively ADP-ribosylated RNA polymerase. Results reveal that T4 early promoters exhibit a bipartite structure, capable of strong interaction with both types of RNA polymerase. The -10, -16, -42 and -52 regions are important for transcript initiation with the native polymerase. To facilitate acceleration of transcription, the ADP-ribosylated enzyme requires not only the integrity of the -10, -16 and -35 regions, but also that of position -33, and even more importantly, maintenance of the upstream promoter element at position -42. The latter positions introduced into the E. coli Ptac promoter render this mutant promoter responsive to Alt-ADP-ribosylated RNA polymerase, like T4 early promoters.

Endoribonuclease RegB from bacteriophage T4 is necessary for the degradation of early but not middle or late mRNAs

The RegB endoribonuclease from bacteriophage T4 cleaves early mRNAs specifically in the middle of the sequence GGAG. We show here that RegB is required for the degradation of bulk T4 early mRNA. In the absence of RegB, the chemical half-life of early transcripts is increased nearly fourfold, whereas their functional half-life is increased twofold. RegB also regulates the translation of several prereplicative genes. The synthesis of several early proteins is down-regulated, probably as a consequence of RegB cleavages in the Shine-Dalgarno sequence of these genes. The synthesis of several other proteins is up-regulated, suggesting that processing by RegB might improve translation by changing the conformation of a transcript. In contrast, RegB does not affect the average half-life of middle and late mRNA. An analysis of the susceptibility to RegB of many GGAG motifs carried by these mRNA species showed that most middle and all late GGAG-carrying mRNAs escape RegB processing in spite of the fact that the enzyme is acting at least until ten minutes post-infection. The sensitivity or resistance to RegB observed during phage infection could be reproduced in uninfected Escherichia coli cells and in vitro. This shows that the GGAG-carrying RNAs that are uncut during T4 infection are not substrates, whatever the period of the T4 cycle when the transcripts are made.

The bacteriophage T4 anti-sigma factor AsiA is not necessary for the inhibition of early promoters in vivo

Bacteriophage T4 early promoters are utilized immediately after infection and are abruptly turned off 2-3 min later (at 30 degrees C) when the middle promoters are activated. The viral early protein AsiA has been suspected to bring about this transcriptional switch: not only does it activate transcription at middle promoters in vivo and in vitro but it also shows potent anti-sigma70 activity in vitro, suggesting that it is responsible for the shut-off of early transcription. We show here that after infection with a phage deleted for the asiA gene the inhibition of early transcription occurs to the same extent and with the same kinetics as in a wild-type infection. Thus, another AsiA-independent circuit efficiently turns off early transcription. The association of a mutation in asiA with a mutation in mod, rpbA, motA or motB has no effect on the inhibition of early promoters, showing that none of these phage-encoded transcriptional regulators is necessary for AsiA-independent shut-off. It is not known whether AsiA is able to inhibit early promoters in vivo, but host transcription is strongly inhibited in vivo upon induction of AsiA from a multicopy plasmid.

Complex Formation of E. coli RNA Polymerase with Bacteriophage T2 DNA: Long-Range Effects in DNA

Conformation behavior of phase T2 DNA in the process of its interaction with it E. coli RNA polymerase was studied using spin labeling technique. T2 DNA was modified by the spin-labeled imidazole at OH-groups of glucosylated cytidine residues. It was shown that the binding of RNA polymerase under the conditions favoring the formation of open promoter complexes induces specific conformational changes in the spin-labeled DNA. The observed conformational changes encompass not only the promoter regions of DNA which are involved in direct contacts with RNA polymerase molecules but extend over remote DNA sites (long-range effect). In relation to this effect, current theoretical models of DNA dynamics are discussed.

Overexpression and structural characterization of the phage T4 protein DsbA

The double strand binding protein A (DsbA) of bacteriophage T4 is one of several viral gene products participating in transcriptional regulation. These proteins interact or associate with the host RNA polymerase core enzyme, enabling the enzyme to successively initiate transcription at different classes of viral promoters: early, middle and late. This leads to a temporally controlled expression of the T4 gene products. The DsbA binding site overlaps the late promoter region, and DsbA binding seems to intensify transcription of late genes in vitro, possibly acting as an enhancer protein (Molecular Biology of Phage T4, Karam, 1994). To further investigate the function and structure of DsbA, we overexpressed the protein in E. coli and purified it to homogeneity. Physiological functionality of the recombinant protein was shown by gel retardation experiments and by circular dichroism (CD) spectroscopy. DsbA shows strong bands in the near UV-CD spectra. The far UV-CD spectroscopy analysis shows alpha-helices to be the main secondary structure elements. This is in agreement with secondary structure predictions. A possible helix-turn-helix motif in the center of the protein could be identified. Results from crosslinking and sedimentation analyses show that DsbA forms a dimer in solution. The thermal unfolding curve fits a dimer-two-state-folding-model, and the unfolding temperature was concentration dependent. Therefore, dimerization should supply the main portion of the free energy of stabilization of deltaG0 = 42 kJ/mol.

A rare type of overlapping genes in bacteriophage T4: gene 30.3' is completely embedded within gene 30.3 by one position downstream

We have previously proposed the existence of one of the rarest types of overlapping genes in bacteriophage T4. We now present the results demonstrating that in a pair of T4 overlapping genes, 30.3 and 30.3', the smaller gene, 30.3', is entirely enclosed within the other by one position downstream. We have constructed plasmids in which different open reading frames from the gene 30.3 region were fused with the 5' end of the lacZ beta-galactosidase (betaGal) gene of Escherichia coli. The gene fusions have been obtained at the position of a HindIII site which was introduced just upstream from the stop codon of gene 30.3'. High betaGal activities have been estimated in the case of plasmids carrying 30.3::lacZ and 30.3'::lacZ fusions. The apparent molecular weights of the fusion proteins, the determined N-terminal sequences, as well as the detected betaGal activities, confirm the structure and arrangement of out-of-phase overlapping genes 30.3 and 30.3'.

ADP-ribosylation and early transcription regulation by bacteriophage T4

Bacteriophage T4 codes at least for two ADP-ribosylating activities, the 76 kDa Alt and the 24 kDa Mod gene products. The main target for both enzymes is the host RNA polymerase. We cloned and sequenced the alt gene and overexpressed the corresponding enzyme. The recombinant protein shows ADP-ribosylating activities in vitro, as had been described earlier for the native enzyme isolated from phage heads. The native as well as the recombinant protein ADP-ribosylate the alpha-subunit of RNA polymerase, but also subunits beta, beta' and sigma 70 and perform an autoribosylation reaction. Taking advantage of the pKWIII test system, constructed to measure promoter strengths in vivo, it was found that ADP-ribosylation of RNA polymerase leads to an increase of transcription from T4 early promoters up to a factor of two. In an infected host cell this should cause an enhanced expression of T4 genes. Depending on whether RNA polymerase was ADP-ribosylated or not, it initiated transcription at T4 promoters with different sequence characteristics: unribosylated RNA polymerase recognizes the early T4 promoters by an extended -10 region, whereas the ribosylated enzyme selects for T4 early promoters with an extended T4-specific and highly conserved -35 region. These results may reflect how the virus, step by step imposes its genetic program on the host cell, and in part they give a rationale for the extension of the consensus sequence observed with these promoters. We also sequenced the genomic region of the T4 mod gene and found two open reading frames coding both for proteins of approximately 24 kDa. Up to now none of the reading frames could be cloned into E. coli in an active form, making it highly probable that the ADP-ribosylation pattern inflicted by gene product Mod on host RNA polymerase is deleterious to these bacteria. Comparisons of the amino acid sequences showed significant homologies among the two reading frames. Computer analysis reveals that both Mod sequences and also the sequence of the Alt protein exhibit a structural concordance with the catalytic domains of other prokaryotic ADP-mono-ribosyltransferases such as the Pseudomonas aeruginosa exotoxin A, the cholera labile enterotoxin, the diphteria toxin, the heat labile enterotoxin A of E. coli, and pertussis toxin. We present a detailed model for T4 transcription regulation.

Identification of a strong promoter of bacteriophage MB78 that lacks consensus sequence around minus 35 region and interacts with phage specific factor

A strong promoter of bacteriophage MB78 does not have minus 35 consensus sequence although it has a TGn motif immediately upstream of minus 10 sequence as well as the AT rich UP element. It is efficiently recognised by the sigma 70 RNA polymerase, however, a phage-specific factor competes with sigma 70 RNA polymerase for binding to this region, the binding of the factor being stronger than that of the polymerase. Contrary to the reports in the literature the polymerase appears not to bind to the UP element whereas the phage-specific factor does. The latter seems to be involved in the regulation of the promoter activity.

Post-transcriptional controls in bacteriophage T4: roles of the sequence-specific endoribonuclease RegB

Gene regB of bacteriophage T4 encodes a sequence-specific endoribonuclease which introduces cuts in early phage messenger RNAs. In most cases, cutting takes place in the middle of the tetranucleotide GGAG. Efficient cleavages occur in the motifs located in intergenic regions, some of them being Shine-Dalgarno sequences. When located in a coding sequence, this tetranucleotide is poorly recognized or not at all. In this article, we have reviewed the properties of the RegB endoribonuclease, with emphasis on its possible roles in T4 development. We show that the nuclease RegB plays at least two roles: (i) it inactivates a sub-class of early mRNA by cleaving Shine-Dalgarno sequences, and (ii) it is necessary for the degradation of early mRNAs, but not of middle and late mRNAs. Accordingly, we found that middle and late mRNAs avoid processing by RegB, probably for different reasons. Most of the middle mRNAs (mRNAs initiated at MotA-dependent promoters) do not contain the motif GGAG in their intergenic regions, whereas about one-third of the late genes have this motif as Shine-Dalgarno sequence. It is not yet known whether the RNase is inactivated early in the phage cycle, or whether it remains active but cannot recognize late mRNAs as substrates.

Evolution of T4-related phages

Much progress has been made in understanding T-even phage biology in the last 50 years. We now know the entire sequence of T4, encoding nearly 300 genes, only 69 of which have been shown to be essential under standard laboratory conditions; no specific function is yet known for about 140 of them. The origin of most phage genes is unclear, and only 42 genes in T4 have significant similarity to anything currently included in GenBank. Comparative analysis of related phages is now being used to gain insight into both the evolutionary origins and interrelationships of these phage genes, and the functions of their protein products. The genomes of phages isolated from Tbilisi hospitals, Long Island sewage plants, the Denver zoo, and Khabarovsk show basic similarity. However, these phages show substantial insertions and deletions in a number of regions relative to each other, and closer investigation of specific sequences often reveals much more complex relationships. There are only a few cases in T4-related phages in which there is evidence for evolution through DNA duplication. These include the fibrous products of genes 12, 34, and 37; head proteins gp23 and gp24; and the Alt enzyme and its downstream neighbors. T4 also contains 13 apparent relatives of group I and group II intron homing endonucleases. Distal portions of the tail fibers of various T-even phages contain segments closely related to tail-fiber regions of other DNA coliphages, such as Mu, P1, P2, and lambda. Horizontal gene transfer clearly emerges as a major factor in the evolution of at least the tail-fiber regions, where site-specific recombination probably is involved in the exchange of host-range determinants.

The DNA-binding domain of the MotA transcription factor from bacteriophage T4 shows structural similarity to the TATA-binding protein

The bacteriophage T4 middle-mode transcription factor MotA consists of two domains of approximately equal size. The C-terminal domain has been shown to contain the DNA-binding elements of the molecule, and the N-terminal domain appears to interact with RNA polymerase. A 12.5-kDa fragment of the C-terminal domain (MotCF), comprising residues 105-211 of MotA, was found to be suitable for structural studies by NMR. The 1H and 15N assignments have been made for MotCF by using two-dimensional homonuclear and heteronuclear experiments. A secondary structure has been determined which consists of a six-stranded antiparallel beta-pleated sheet with three alpha-helical segments. The secondary structure of MotCF has a clear similarity to one half of the eukaryotic TATA-binding protein (TBP), which is an intramolecular dimer. Therefore, MotCF may be related to a monomeric ancestral protein of TBP. TBP binds its target DNA in the minor groove by specific interactions with hydrophobic and aromatic residues on the exposed sheet surface of the protein. Similar residues are also present on the beta-sheet surface of MotCF, suggesting that it too binds DNA in the minor groove.

Cloning and expression of genes from the genomic region between genes cd and 30 of bacteriophage T4

Ten open reading frames (ORFs) from the cd-30 region of bacteriophage T4, as well as genes 31 and rIII, have been cloned, and all were found to be expressed in a T7 RNA polymerase system. Expression data confirm the existence of genes 31.2, 31.1, 31, rIII, 30.9, 30.8, 30.7, 30.6, 30.5, 30.4, 30.3 and 30.2, which predict peptides of 78, 102, 111, 82, 58, 110, 121, 95, 65, 68, 152 and 278 amino acids (aa), respectively. The major product of gene 30.9 is a basic peptide initiated at the second AUG codon that is found 42 nucleotides downstream and in frame from the first AUG. A plasmid carrying gene 30.3 expresses two different peptides, one of which is of the size predicted for gp30.3. By site-directed mutagenesis we have shown that the smaller peptide is encoded by gene 30.3' which is completely embedded within gene 30.3, but in a different reading frame. Gene 30.3' encodes a 75-aa basic peptide with its C terminus rich in charged aa.

Direct PCR sequencing of the ndd gene of bacteriophage T4: identification of a product involved in bacterial nucleoid disruption

The rapid disruption of the Escherichia coli nucleoid after T4 infection requires the activity of the phage-encoded ndd gene. We have genetically identified the sequence encoding ndd. Determination of the sequence of a 2.5-kb segment including ndd closed the last significant gap in the sequence of the T4 genome. This analysis was performed on PCR-amplified fragments that were purified by gel-exclusion chromatography and then submitted to linear amplification cycle sequencing. This technology permitted sequence comparison of two ndd mutants (ndd44 and ndd98) with the wild-type gene. The analysis of ndd from six bacteriophages of the T-even family indicated that the protein encoded by this nonessential gene is surprisingly conserved.

Identification of bacteriophage T4 prereplicative proteins on two-dimensional polyacrylamide gels

Bacteriophage T4 makes a large number of prereplicative proteins, which are involved in directing the transition from host to phage functions, in producing the new T4 DNA, and in regulating transcriptional shifts. We have used two-dimensional gel electrophoresis (nonequilibrium pH gradient electrophoresis gels in the first dimension and sodium dodecyl sulfate-polyacrylamide gradient slab gels in the second) to identify a number of new prereplicative proteins. The products of many known genes are identified because they are missing in mutants with amber mutations of those genes, as analyzed by us and/or by previous workers. Some have also been identified by running purified proteins as markers on gels with labeled extracts from infected cells. Other proteins that are otherwise unknown are characterized as missing in infections with phage carrying certain large deletions and, in some cases, are correlated with sequence data.

The asiA gene of bacteriophage T4 codes for the anti-sigma 70 protein

The anti-sigma 70 factor of bacteriophage T4 is a 10-kDa (10K) protein which inhibits the sigma 70-directed initiation of transcription by Escherichia coli RNA polymerase holoenzyme. We have partially purified the anti-sigma 70 factor and obtained the sequence of a C-terminal peptide of this protein. Using reverse genetics, we have identified, at the end of the lysis gene t and downstream of an as yet unassigned phage T4 early promoter, an open reading frame encoding a 90-amino-acid protein with a predicted molecular weight of 10,590. This protein has been overproduced in a phage T7 expression system and partially purified. It shows a strong inhibitory activity towards sigma 70-directed transcription (by RNA polymerase holoenzyme), whereas it has no significant effect on sigma 70-independent transcription (by RNA polymerase core enzyme). At high ionic strength, this inhibition is fully antagonized by the neutral detergent Triton X-100. Our results corroborate the initial observations on the properties of the phage T4 10K anti-sigma 70 factor, and we therefore propose that the gene which we call asiA, identified in the present study, corresponds to the gene encoding this T4 transcriptional inhibitor.

Role of MotA transcription factor in bacteriophage T4 DNA replication

At least two bacteriophage T4 replication origins, ori(uvsY) and ori(34), contain a T4 middle-mode promoter that is necessary for origin function. We wanted to analyze the requirement of these two replication origins for the MotA protein, which is the phage-encoded activator of middle-mode promoters. To ensure the complete absence of MotA protein, we deleted the motA gene from the T4 genome. Unexpectedly, the deletion mutant was not viable unless the MotA protein was provided from a recombinant plasmid. Therefore, MotA is an essential protein for T4 growth. The motA delta mutation reduced the synthesis of several proteins that are encoded by genes with middle-mode promoters, delayed and reduced the synthesis of late proteins, and substantially reduced phage genomic replication. The motA delta mutation also reduced the replication of an ori(uvsY)-containing plasmid and virtually abolished replication of an ori(34)-containing plasmid. The replication defects of the two origins correlated with transcriptional defects: the motA delta mutation modestly reduced transcription from the plasmid-borne ori(uvsY) promoter and strongly reduced transcription from the ori(34) promoter. These results provide strong evidence that MotA protein is normally involved in origin-dependent replication. However, MotA is not required for origin-directed replication as long as transcription can occur from the origin promoter.

Sequence and characterization of the bacteriophage T4 comC alpha gene product, a possible transcription antitermination factor

We have sequenced a 1,340-bp region of the bacteriophage T4 DNA spanning the comC alpha gene, a gene which has been implicated in transcription antitermination. We show that comC alpha, identified unambiguously by sequencing several missense and nonsense mutations within the gene, codes for an acidic polypeptide of 141 residues, with a predicted molecular weight of 16,680. We have identified its product on one- and two-dimensional gel systems and found that it migrates abnormally as a protein with a molecular weight of 22,000. One of the missense mutations (comC alpha 803) is a glycine-to-arginine change, and the resulting protein exhibits a substantially faster electrophoretic mobility. The ComC alpha protein appears immediately after infection. Its rate of synthesis is maximum around 2 to 3 min postinfection (at 37 degrees C) and then starts to decrease slowly. Some residual biosynthesis is still detectable during the late period of phage development.

Deoxyuridylate-hydroxymethylase of bacteriophage SPO1

Phage SPO1 of Bacillus subtilis carries hydroxymethyl-deoxyuridylate in place of thymidylate in its DNA. The enzyme, responsible for the conversion of dUMP to HmdUMP, is a dUMP hydroxymethylase, encoded by the SPO1 gene 29. Here we describe the cloning and sequencing of the gene and the overexpression of the gene product. DNA hybridization using the DNA of bacteriophage T4 dCMP-hydroxymethylase gene as a probe, allowed us to identify and map g29 on a 3.9-kb restriction fragment, EcoRI*11. We determined the nucleotide sequence. One of the open reading frames detected, coding for a putative 44.6-kDa protein, showed significant amino acid homologies with all known thymidylate synthases. Gp29 was overexpressed in the pT7 system. Extracts prepared from induced cells show hydroxymethylase activity in a tritium release assay.

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.

The nucleotide sequence between genes 31 and 30 of bacteriophage T4

The nucleotide sequence of the 2994 bp T4 phage DNA fragment between genes 31 and 30 is presented. The fragment contains 7 complete open reading frames in the direction of early transcription and two early promoters, PE128.6 and PE128.2, which we show to cause difficulties in cloning DNA from this genomic region. Our data complete the nucleotide sequence and the organization of genes in the genomic region between T4 genes 31 and 30.

Two bacteriophage T4 base plate genes (25 and 26) and the DNA repair gene uvsY belong to spatially and temporally overlapping transcription units

The bacteriophage T4 DNA recombination-repair gene uvsY located at or near an origin of DNA replication and adjacent to the late base plate genes 25 and 26. Our present results reveal a complex transcription pattern in the region encompassing these genes. Most significantly, uvsY and two ORFs, downstream of it, all of which are transcribed from a middle promoter before the onset of DNA replication, are also part of a larger late transcription unit which includes the base plate genes 25 and 26. The late genes 25 and 26 are transcribed not only late, but also early from one or several early promoters further upstream. Translation, however, is inhibited by secondary structures which sequester the ribosome binding site in the early transcript. We discuss possible advantages of these transcriptional patterns for T4 DNA recombination, replication, and repair. The predicted and in vivo-expressed 23.9-kDa product of gene 26 is smaller than the reported size of gene 26 protein isolated from base plates, suggesting that nascent gp26 might be processed to a larger protein during assembly.

Gene product dsbA of bacteriophage T4 binds to late promoters and enhances late transcription

Gene product 33 of phage T4 is known to be essential in late transcription. Upstream from gene 33 and overlapping its 5' terminal sequence by 20 bp, we identified an open reading frame coding for a binding protein for double-stranded DNA (DsbA). Gene product DsbA is composed of 89 amino acid residues with a Mr of 10376 kDa. We purified this protein to homogeneity from over-expressing cells. Gel retardation assays reveal that it binds to DNA and footprint analyses disclose that it interacts preferentially with T4 late promoter regions. At the sites of binding the protein introduces nicks in double-stranded DNA. In vitro transcription assays performed with T4 late modified RNA polymerase on restriction fragments harbouring a T4 late promoter region prove that gene product DsbA enhances transcription from these promoter regions in the presence of gene product 33. Gene dsbA is distinct from gene das which maps close to this genomic region.

Gene 32 transcription and mRNA processing in T4-related bacteriophages

We have analysed transcription and mRNA processing for the gene 32 region of five phages related to T4. Two different organizations of gene 32 proximal promoters were found. In T4 and M1, middle- and late-mode promoters are separated by 50 nucleotides and located within an upstream open reading frame. In T2, K3, Ac3, and Ox2, the 626bp T4 sequence that includes these promoters is replaced by a 59bp sequence containing overlapping middle and late promoters. The RNase E-dependent processing of the g32 mRNAs is conserved in all of the phages. The processing site immediately upstream of g32 in T4 and M1 has been replaced in the other phages by a different sequence that is also cleaved by RNase E. The remarkable conservation of these regulatory features, despite the sequence divergences, suggests that they play an important role in the control of gene expression.

Bacteriophage T4 nrdA and nrdB genes, encoding ribonucleotide reductase, are expressed both separately and coordinately: characterization of the nrdB promoter

We examined the expression of the bacteriophage T4 nrdA and nrdB genes, which encode the alpha 2 and beta 2 subunits, respectively, of ribonucleoside diphosphate reductase, the first committed enzyme in the pathway of synthesis of the deoxyribonucleoside triphosphates. T4 nrdA, located 700 bp upstream from nrdB, has been shown previously to be transcribed by two major transcripts: a prereplicative, polycistronic message, TU, orginating at an immediate-early promoter, PE, that is 3.5 kb upstream from nrdA, and a postreplicative message commencing from a late promoter in its 5' flank. We have found a third promoter initiating a transcript at 159 nucleotides upstream from the reading frame of nrdB. PnrdB functions only in the presence of the T4 motA gene product, which is required for middle (time) promoters, and therefore the onset of nrdB transcription is delayed more than 2 min after infection. Because of the distance of nrdA from PE, the inception of nrdA transcription (delayed early) coincides closely with that of nrdB. An apparent termination site, tA, occurs about 80 bp downstream from nrdA. Some of the polycistronic mRNA reading through the site after 5 min contributes to nrdB transcription. nrdA and nrdB genes in an uninfected host have been reported to be transcribed only coordinately. In contrast, T4 nrdA and nrdB are initially transcribed separately onto the PE and PnrdB transcripts, respectively, but at about 5 min after infection are transcribed both coordinately and on separate transcripts. Evidence is presented that TU coordinately transcribes a deoxyribonucleotide operon in the order: frd, td, gene 'Y,' nrdA, nrdB. Since the beta 2 subunit is known to be formed after the alpha 2 subunit, the expression of the nrdB gene determines the onset of deoxyribonucleoside triphosphate synthesis and thus of T4 DNA replication.

Nucleotide sequence and control of transcription of the bacteriophage T4 motA regulatory gene

A 2116bp segment of the bacteriophage T4 genome encompassing the motA regulatory gene has been sequenced. In addition to motA, five open reading frames were identified in the direction of early transcription. The motA gene encodes a basic protein of 211 amino acids with a predicted molecular weight of 23,559. Measurements of the rate of transcription of motA showed that the promoter of this gene is turned off after only 2 min of T4 development. This early promoter presents a structure which is richer in information than that of a classical constitutive Escherichia coli promoter. In addition to containing conserved sequences centred at -10 and -35, this promoter shares extensive homologies with other subgroups of early promoters in regions centred at +3 and at -55. We discuss the possible role of these different sequence determinants.

Nucleotide sequence of bacteriophage T4 gene 31 region

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An RNA polymerase-binding protein that is required for communication between an enhancer and a promoter

Although bacteriophage T4 late promoters are selectively recognized by Escherichia coli RNA polymerase bearing a single protein encoded by T4 gene 55 (gp55), efficient transcription at these promoters requires enhancement by the three T4 DNA polymerase accessory proteins, bound to distal "mobile enhancer" sites. Two principles are shown to govern this transcriptional enhancement: (i) Promoter recognition and communication between the enhancer and the promoter require separate phage-coded proteins. Only RNA polymerase that has the T4 gene 33 protein (gp33) bound to it is subject to enhancement by the three DNA replication proteins. (ii) Transcriptional enhancement in this prokaryotic system is promoter-specific. Promoter specificity is generated by a direct competition of phage T4 gp33 and gp55 with the E. coli promoter recognition protein, sigma 70, for binding to the E. coli RNA polymerase core. Thus, polymerase that contains sigma 70 is competent to transcribe T4 early and middle genes, but lacks the ability to be enhanced by the DNA replication proteins, while polymerase that contains gp55 and gp33 is capable of enhancement via gp33, but its activity is restricted to T4 late promoters by gp55.

The bacteriophage T4 gene mrh whose product inhibits late T4 gene expression in an Escherichia coli rpoH (sigma 32) mutant

In an Escherichia coli rpoH mutant (affecting sigma 32, heat-shock sigma factor) infected at high temperatures with wild-type T4 phage, late T4 transcription and consequently progeny production are dramatically impaired. This defect is due, in part, to insufficient activity of sigma 70 [Frazier and Mosig, J. Bacteriol. 170 (1988) 1384-1388], which is necessary to initiate early T4 transcription. Unexpectedly, however, we found that, in this rpoH host, late T4 transcription is also impaired when the temperature is raised from 30 to 42 degrees C late after infection, when T4 transcription is directed by the T4-encoded sigma factor, sigma gp55. Here, we show that a T4 gene that we call mrh (modulates rpoH), located at 14 kb on the T4 map, is responsible for the inhibition of late T4 transcription in the rpoH mutant host. T4 deletion mutants that lack the mrh gene can produce progeny in the rpoH host, but the Mrh protein, provided in trans from a plasmid-borne mrh gene, inhibits this growth. We have cloned and sequenced this T4 gene and synthesized the Mrh protein in a T7 RNA polymerase-dependent expression system. The Mr of the Mrh protein deduced from the nucleotide sequence is 13419. Gene mrh is cotranscribed with several other, yet unidentified genes, both from an early promoter downstream from the late soc gene (encoding the small outer capsid protein) and from the late soc promoter further upstream.(ABSTRACT TRUNCATED AT 250 WORDS)

Transcription and messenger RNA processing upstream of bacteriophage T4 gene 32

Bacteriophage T4 gene 32 lies at the 3' end of a complex transcription unit which includes genes 33, 59, and several open reading frames. In the course of an infection, four major transcripts are synthesized from this unit: two overlapping polycistronic transcripts about 3800 and 2800 nucleotides in length, and two monocistronic gene 32 transcripts about 1150 and 1100 nucleotides in length. These transcripts are made at different times in infection and the polycistronic transcripts have segmental differences in stability. Messenger RNA processing yields a 1025 nucleotide monocistronic gene 32 transcript, and a 135 nucleotide transcript containing part of the gene 59 coding sequence. Processing depends on Escherichia coli encoded ribonuclease E. This pattern of transcription and processing leads to the synthesis of gene 32 mRNA throughout infection, whereas transcripts encoding the upstream genes are present only early in infection. The 3800 nucleotide polycistronic transcript initiates at a promoter that does not require T4 encoded factors for activity. However, full-length synthesis of this transcript depends on the T4 mot gene product. The region upstream of gene 32 also contains four E. coli-like promoters that are active on chimeric plasmids in uninfected cells, but inactive in bacteriophage T4. The location of these cryptic T4 promoters is intriguing in that they lie near the 5' ends of open reading frame B, gene 59 and gene 32. They could play a role in phage development under particular conditions of growth or in bacterial hosts other than those examined here.