Constitutive expression of a transcription termination factor by a repressed prophage: promoters for transcribing the phage HK022 nun gene

Hybrid Vigor: Importance of Hybrid λ Phages in Early Insights in Molecular Biology

Laboratory-generated hybrids between phage λ and related phages played a seminal role in establishment of the λ model system, which, in turn, served to develop many of the foundational concepts of molecular biology, including gene structure and control. Important λ hybrids with phages 21 and 434 were the earliest of such phages. To understand the biology of these hybrids in full detail, we determined the complete genome sequences of phages 21 and 434. Although both genomes are canonical members of the λ-like phage family, they both carry unsuspected bacterial virulence gene types not previously described in this group of phages. In addition, we determined the sequences of the hybrid phages λ imm21, λ imm434, and λ h434 imm21. These sequences show that the replacements of λ DNA by nonhomologous segments of 21 or 434 DNA occurred through homologous recombination in adjacent sequences that are nearly identical in the parental phages. These five genome sequences correct a number of errors in published sequence fragments of the 21 and 434 genomes, and they point out nine nucleotide differences from Sanger's original λ sequence that are likely present in most extant λ strains in laboratory use today. We discuss the historical importance of these hybrid phages in the development of fundamental tenets of molecular biology and in some of the earliest gene cloning vectors. The 434 and 21 genomes reinforce the conclusion that the genomes of essentially all natural λ-like phages are mosaics of sequence modules from a pool of exchangeable segments.

Phage integration alters the respiratory strategy of its host

Temperate bacteriophages are viruses that can incorporate their genomes into their bacterial hosts, existing there as prophages that refrain from killing the host cell until induced. Prophages are largely quiescent, but they can alter host phenotype through factors encoded in their genomes (often virulence factors) or by disrupting host genes as a result of integration. Here we describe another mechanism by which a prophage can modulate host phenotype. We show that a temperate phage that integrates in Escherichia coli reprograms host regulation of an anaerobic respiratory system, thereby inhibiting a bet hedging strategy. The phage exerts this effect by upregulating a host-encoded signal transduction protein through transcription initiated from a phage-encoded promoter. We further show that this phenomenon occurs not only in a laboratory strain of E. coli, but also in a natural isolate that contains a prophage at this site.

Animals and plants can all fall prey to viruses – and so can bacteria. The viruses that infect bacteria are called bacteriophages (or phages for short), and they are found everywhere bacteria live and probably outnumber bacteria by at least ten to one.

While some phages quickly kill every bacterial cell they infect, others enter a dormant state by inserting their DNA into the DNA of their host cell. Here they lie in wait for a signal that reactivates them, triggering the production of more phages and the death of the host cell. While the phage lies dormant its DNA may harm the host by interfering with nearby bacterial genes, or it may actually provide new genes that benefit the host. In most cases the effects of dormant phages are unknown.

A bacterium known as Escherichia coli is commonly found in the intestines of humans and other mammals. It can use a nutrient called trimethylamine oxide (TMAO) to help it survive rapid decreases in oxygen levels that can occur in its environment. When a phage called HK022 infects E. coli, the phage enters a dormant state by inserting its DNA between two genes that are critical for E. coli to use TMAO. However, it is not clear what effect, if any, HK022 has on E. coli’s behavior.

To address this question, Carey et al. used genetic approaches to study E. coli cells carrying dormant HK022 phages. The experiments showed that the bacteria lost the ability to use TMAO to survive rapid decreases in oxygen because the dormant phages switched on one of the neighboring E. coli genes. Unexpectedly, the phage achieved this by neatly replacing the gene’s own promoter – the stretch of DNA that contains information about when the gene should be switched on, and how strongly – with a substitute promoter carried in the phage’s DNA. This substitute promoter is stronger than the normal version – meaning that the gene is more active than it should be.

Phages are key players in every natural population of microbes and are therefore entwined in the health of humans and the environment. The findings of Carey et al. show a new mechanism through which phages modify their hosts. In the future it may be possible to develop this mechanism into a tool to manipulate bacteria in complex environments like infection sites, for example by introducing phages that block the mechanisms that allow bacteria to tolerate antibiotics.

Structural basis of transcription arrest by coliphage HK022 Nun in an Escherichia coli RNA polymerase elongation complex

Coliphage HK022 Nun blocks superinfection by coliphage λ by stalling RNA polymerase (RNAP) translocation specifically on λ DNA. To provide a structural framework to understand how Nun blocks RNAP translocation, we determined structures of Escherichia coli RNAP ternary elongation complexes (TECs) with and without Nun by single-particle cryo-electron microscopy. Nun fits tightly into the TEC by taking advantage of gaps between the RNAP and the nucleic acids. The C-terminal segment of Nun interacts with the RNAP β and β’ subunits inside the RNAP active site cleft as well as with nearly every element of the nucleic acid scaffold, essentially crosslinking the RNAP and the nucleic acids to prevent translocation, a mechanism supported by the effects of Nun amino acid substitutions. The nature of Nun interactions inside the RNAP active site cleft suggests that RNAP clamp opening is required for Nun to establish its interactions, explaining why Nun acts on paused TECs.

DOI:http://dx.doi.org/10.7554/eLife.25478.001

RNA polymerase elongation factors

The elongation phase of transcription by RNA polymerase is highly regulated and modulated. Both general and operon-specific elongation factors determine the local rate and extent of transcription to coordinate the appearance of transcript with its use as a messenger or functional ribonucleoprotein or regulatory element, as well as to provide operon-specific gene regulation.

Overexpression of phage HK022 Nun protein is toxic for Escherichia coli

The Nun protein of coliphage HK022 excludes superinfecting lambda phage. Nun recognizes and binds to the N utilization (nut) sites on phage lambda nascent RNA and induces transcription termination. Overexpression of Nun from a high-copy plasmid is toxic for Escherichia coli, despite the fact that nut sites are not encoded in the E. coli genome. Cells expressing Nun cannot exit stationary phase. Toxicity is related to transcription termination, since host and nun mutations that block termination also suppress cell killing. Nun inhibits expression of wild-type lacZ, but not lacZ expressed from the Crp/cAMP-independent lacUV5 promoter. Microarray and proteomic analyses show that Nun down-regulates crp and tnaA. Crp overexpression and high indole concentrations partially reverse Nun-mediated toxicity and restore lacZ expression.

Interplay between the temperate phages PY54 and N15, linear plasmid prophages with covalently closed ends

The objective of this study was to determine whether the temperate Yersinia enterocolitica phage PY54 may interact with the related Escherichia coli phage N15 during both the lysogenic and the lytic cycle in the same cell. The PY54 and N15 prophages are linear plasmids which have been shown to be compatible and stably replicating in E. coli and Yersinia. In E. coli, the PY54 prophage does not restrict N15 propagation. In contrast, N15 reduces by use of its cor gene the susceptibility of Yersinia strains to PY54. Doubly lysogenic E. coli strains release PY54 virions, some of which apparently contain the N15 genome. Further experiments with replicative miniplasmid derivatives of PY54, N15, and the related Klebsiella oxytoca phage phiKO2 demonstrated that the phiKO2 and N15 plasmid prophages belong to the same incompatibility group.

Protection of antiterminator RNA by the transcript elongation complex

Nascent transcripts encoded by the putL and putR sites of phage HK022 bind the transcript elongation complex and suppress termination at downstream transcription terminators. We report here that the chemical stability of putL RNA is considerably greater than that of the typical Escherichia coli message because the elongation complex protects this RNA from degradation. When binding to the elongation complex was prevented by mutation of either putL or RNA polymerase, RNA stability decreased more than 50-fold. The functional modification conferred by putL RNA on the elongation complex is also long-lived: the efficiency of terminator suppression remained high for at least 10 kb from the putL site. We find that RNase III rapidly and efficiently cleaved the transcript just downstream of the putL sequences, but such cleavage changed neither the stability of putL RNA nor the efficiency of antitermination. These results argue that the continuity of the RNA that connects put sequences to the growing point is not required for persistence of the antiterminating modification in vivo.

Suppression of factor-dependent transcription termination by antiterminator RNA

Nascent transcripts of the phage HK022 put sites modify the transcription elongation complex so that it terminates less efficiently at intrinsic transcription terminators and accelerates through pause sites. We show here that the modification also suppresses termination in vivo at two factor-dependent terminators, one that depends on the bacterial Rho protein and a second that depends on the HK022-encoded Nun protein. Suppression was efficient when the termination factors were present at physiological levels, but an increase in the intracellular concentration of Nun increased termination both in the presence and absence of put. put-mediated antitermination thus shows no apparent terminator specificity, suggesting that put inhibits a step that is common to termination at the different types of terminator.

The N-terminus is unstructured, but not dynamically disordered, in the complex between HK022 Nun protein and lambda-phage BoxB RNA hairpin

The Nun protein of lambdoid phage HK022 excludes lambda-phage superinfection by blocking expression of genes downstream from the lambda nut sequences. Heteronuclear NMR studies have been performed on a Nun peptide comprising residues 1-49 bound to the nutR BoxB RNA. The pattern of (13)C chemical shifts indicates that the arginine-rich motif of Nun forms an induced alpha-helix, consisting of residues 23-43, when bound to BoxB RNA, consistent with the structure of a shorter (residues 22-44) Nun peptide/BoxB RNA complex [Faber, C., Schärpf, M., Becker, T., Sticht, H. and Rösch (2001) J. Biol. Chem. 276, 32064-32070]. The N-terminal extension, residues 1-22, does not show chemical shifts or nuclear Overhauser effects characteristic of stable secondary structure. Nonetheless, (15)N relaxation measurements indicate that this region is not completely disordered, as expected for a random coil peptide. Restriction of conformation flexibility in the N-terminal extension of Nun may be important for binding to other target molecules involved in transcription termination.