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Summary

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of bacteriophage–host interactions
  5. Bacteriophage–host interactions direct transcription in phage T4-infected cells
  6. Bacteriophage–host interactions assist transcription in phage T7-infected cells
  7. Bacteriophage–host interactions influencing replication of the host cell
  8. Do phages influence the translation apparatus?
  9. Bacteriophage–host interactions protect the phage genome from degradation
  10. Influence of bacteriophage–host interactions on proteolysis
  11. Discussion and applications
  12. References

Interactions between bacteriophage proteins and bacterial proteins are important for efficient infection of the host cell. The phage proteins involved in these bacteriophage–host interactions are often produced immediately after infection. A survey of the available set of published bacteriophage–host interactions reveals the targeted host proteins are inhibited, activated or functionally redirected by the phage protein. These interactions protect the bacteriophage from bacterial defence mechanisms or adapt the host-cell metabolism to establish an efficient infection cycle. Regrettably, a large majority of bacteriophage early proteins lack any identified function. Recent research into the antibacterial potential of bacteriophage–host interactions indicates that phage early proteins seem to target a wide variety of processes in the host cell – many of them non-essential. Since a clear understanding of such interactions may become important for regulations involving phage therapy and in biotechnological applications, increased scientific emphasis on the biological elucidation of such proteins is warranted.


Introduction

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of bacteriophage–host interactions
  5. Bacteriophage–host interactions direct transcription in phage T4-infected cells
  6. Bacteriophage–host interactions assist transcription in phage T7-infected cells
  7. Bacteriophage–host interactions influencing replication of the host cell
  8. Do phages influence the translation apparatus?
  9. Bacteriophage–host interactions protect the phage genome from degradation
  10. Influence of bacteriophage–host interactions on proteolysis
  11. Discussion and applications
  12. References

Bacteriophages, like all viruses, are absolute parasites. Although their genome encodes all the proteins of the phage particle, bacteriophages rely heavily on the host cell for their reproduction. Their infection process involves a number of tightly programmed steps: adsorption on the host cell, internalization of the genome (the stage after which temperate phages can become quiescent), transition of a host to a phage-directed metabolism, replication of the phage genome, morphogenesis and finally packaging and host-cell lysis (Guttman et al., 2005).

Interactions between phage-encoded and bacterial proteins inside the infected cell are important for efficient infection of the host cell. This review specifically addresses these interactions, which are referred to as bacteriophage–host interactions. Apart from protein–protein interactions, associations with nucleic acids (DNA or RNA), phage–receptor interactions or even the binding of lysins to their substrate (peptidoglycan) and many other interactions could be classified as bacteriophage–host interactions. Although important to various stages of the infection cycle, these other types of interactions fall outside the scope of this review.

A survey of described bacteriophage–host interactions reveals that the targeted host proteins are inhibited, activated or redirected to another function by specific phage proteins (Table 1). Through these interactions, the bacteriophage adapts the host-cell metabolism to establish an efficient infection cycle and directs some components of the host-cell machinery towards production of new virions (Kutter et al., 1994; 2005; Miller et al., 2003; Guttman et al., 2005). Since most phages use the transcription apparatus of the host at some stage during the infection cycle, the RNA polymerase is a common target for phage proteins (Table 1). The replication machinery also serves as a target. Other evidence suggests an impact on the translation machinery, although the mechanisms involved and functional outcome remain elusive. In addition, some bacteriophage–host interactions protect the bacteriophage from bacterial defence mechanisms (e.g. inhibition of restriction enzymes and proteases). Although these bacteriophage–host interactions are involved in all stages of the infection cycle, most interactions are hypothesized to take place during the transition to a phage-oriented metabolism early in the infection cycle (Miller et al., 2003; Guttman et al., 2005). Indeed, our survey reveals that the majority (64%) of bacteriophage–host interactions involve phage early proteins (Table 1 and Fig. 1). Delayed early proteins and middle proteins take part in 7% and 25% of bacteriophage–host interactions respectively. Late proteins (4%) involved in bacteriophage–host interactions are structural proteins that are internalized along with the phage genome and exert their influence during the early stages of infection.

Table 1.  Overview of the known bacteriophage–host interactions.
PhagePhage proteinHost proteinModEffectLengthStageReference
  • a.

    Because the N- and C-terminal domain of bacteriophage T7 gp0.7 have separable functions the length of each domain is indicated.

  • b.

    U, this property is unknown.

  • c.

    Bacteriophage T4 protein Alt and IPI* are internal head proteins injected into the host cell along with the phage genome. Although they are late proteins they exert their effect early during infection.

  • For each bacteriophage–host interaction the bacteriophage protein and the phage it originates from as well as the host protein are shown. Mod indicates the involvement of modification in a particular bacteriophage–host interaction (P, −P and R being phosphorylation, dephosphorylation and ribosylation of the host protein respectively). If known, the effect of the bacteriophage–host interaction is summarized along with the length of the phage protein and its stage of production in the infection cycle.

T7gp0.3Type I restriction endonucleases Protection of the genome from restriction117EarlyWalkinshaw et al. (2002)
gp0.7 C-termRNA polymerase (RNAP) β′ subunit Host transcription shutoff117aEarlyMichalewicz and Nicholson (1992)
gp0.7 N-termRNAP β and β′ subunitPEfficiency of termination242aEarlySeverinova and Severinov (2006)
RNase IIIPProcessing of T7 mRNA  Mayer and Schweiger (1983)
RNase E and RhlBPProtection of T7 mRNA from degradation  Marchand et al. (2001)
Translation initiation and elongation factorsPUb  Robertson et al. (1994)
gp2RNAP β′ subunit Inhibition of transcription initiation64MiddleNechaev and Severinov (1999)
gp1.2dGTPase Inhibition of the dGTPase85EarlyHuber et al. (1988)
gp5Thioredoxine Processivity factor of the DNA polymerase704MiddleTabor et al. (1987)
gp5.5H-NS Inhibits H-NS99MiddleLiu and Richardson (1993)
gp5.9RecBCD nuclease Inhibits nuclease and ATPase activity52MiddleMolineux (2005)
T4AltOne RNAP α subunit (28 targets in total)RPreferential expression of T4 early genes675LatecSommer et al. (2000); Depping et al. (2005)
AlcRNAP β subunit (postulated) Host transcription shutoff167EarlyKashlev et al. (1993)
ModABoth RNAP α subunits (4 targets in total)RLower expression of T4 early and host genes200EarlySkórko et al. (1977)
 ModBS1 ribosomal protein, trigger factor, EF-Tu (8 targets in total)RUb207EarlyDepping et al. (2005)
AsiAσ70 factor Inhibits recognition of σ70 promoters90EarlyOuhammouch et al. (1995)
MotAσ70 factor Recognition of T4 middle promoters211EarlyOuhammouch et al. (1995)
gp55RNAP core enzyme σ factor for expression from late promoters185MiddleKassavetis et al. (1983)
gp33RNAP core enzyme Helper of gp55112MiddleKassavetis et al. (1983)
RpbARNAP core enzyme Favours expression of T4 late genes (postulated)129Early/ middleKolesky et al. (1999)
Mrhσ32−PDecoy of σ32 from RNAP core (postulated)161EarlyMosig et al. (1998)
SrhRNAP core enzyme (postulated) Decoy of σ32 from RNAP core (postulated)67EarlyMosig et al. (1998)
SrdRNAP core enzyme (postulated) Decoy of σ7038 from RNAP core (postulated)248EarlyMosig et al. (1998)
ArnRglB (MrcBC) Protection of the T4 genome from restriction129EarlyDharmalingam et al. (1982)
IPI*GmrS-GmrD Protection of the T4 genome from restriction76LatecBair et al. (2007)
gp31GroEL Correct folding of gp23111MiddleRichardson et al. (1998)
PinALon protease Inhibition of protease activity161EarlySkorupski et al. (1988)
τ (Vs)Valyl-tRNA synthetase Possible stabilization of the synthetase115EarlyMüller and Marchin (1977)
StpPrrC Inhibition of restriction29EarlyPenner et al. (1995)
NddHU Role in disruption of the host genome151EarlyMiller et al. (2003)
N4SSBRNAP β′ subunit Activation of late transcription265MiddleMiller et al. (1997)
λPDnaB (DNA helicase) Initiation of λ genome replication233Delayed earlyLiberek et al. (1988)
NRNAP core, NusA, NusG Antitermination, delayed early transcription133EarlyMason and Greenblatt (1991)
QRNAP holoenzyme (core +σ70) Antitermination, late transcription207Delayed earlyMarr et al. (2001)
λGamRecBCD Inhibits nuclease and helicase activity of RecBCD138Delayed earlyCourt et al. (2007)
RalHsdM or/and HsdS (postulated) Protection of the genome from restriction66EarlyLoenen and Murray (1986)
CIIIFtsH Inhibition of the protease activity54EarlyKobiler et al. (2007)
phiEco32gp36RNAP core σ factor (recognition of phage promoters)214UbSavalia et al. (2008)
gp79RNAP core Inhibition of σ70-dependent transcription82UbSavalia et al. (2008)
P2BDnaB (DNA helicase) Initiation of P2 genome replication166EarlyOdegrip et al. (2000)
OrgRNAP α subunit Initiation of late transcription72EarlyWood et al. (1997)
φ29p56Uracil-DNA glycosylase Inhibition of uracil-DNA glycosylase56EarlySerrano-Heras et al. (2007)
PBS2UgiUracil-DNA glycosylase Protects phage from degradation84EarlyPutnam and Tainer (2005)
SPO1gp44 (E3)RNAP β subunit Inhibition of the host RNAP237EarlyWei and Stewart (1995)
gp28RNAP core enzyme σ factor for middle transcription220EarlyLosick and Pero (1981)
gp33RNAP core enzyme σ factor for late transcription101MiddleLosick and Pero (1981)
gp34RNAP core enzyme Helper protein for late transcription197MiddleLosick and Pero (1981)
Xp10p7RNAP β′ subunit Inhibition and antitermination of transcription73EarlyYuzenkova et al. (2008)
77gp104DnaI (helicase loader) Shutoff of host replication52UbLiu et al. (2004)
Ubgp016DnaI (helicase loader) Shutoff of host replication297UbLiu et al. (2004)
Ubgp025DnaN (DNA Pol III β subunit) Shutoff of host replication58UbLiu et al. (2004)
Twortgp168DnaN (DNA Pol III β subunit) Shutoff of host replication74UbLiu et al. (2004)
G1gp240DnaN (DNA Pol III β subunit) Shutoff of host replication58UbLiu et al. (2004)
Ubgp078DnaG (DNA primase) Shutoff of host replication71UbLiu et al. (2004)
Ubgp140PT-R14 (involved in replication) Shutoff of host replication101UbLiu et al. (2004)
Ubgp67Component of RNAP Shutoff of host transcriptionUbUbLiu et al. (2004)
PA16gp106DnaN (DNA Pol III β subunit) Shutoff of host replication (postulated)132UbBelley et al. (2006)
image

Figure 1. A survey of the currently described bacteriophage–host interactions. These graphs are based on the bacteriophage–host interactions listed in Table 1. A. The histogram displays the length distribution of the phage proteins involved in bacteriophage–host interactions in absolute numbers. The relative amount is indicated above each group. The average length of the bacteriophage proteins targeting host-cell proteins is 157 residues. This number drops to 135 residues if T7 DNA polymerase and T4 Alt – two proteins that are exceptionally large compared with the other phage proteins – are excluded. The lower limit of each size group is indicated, whereas the upper limit can be inferred from the lower limit of the successive size. B. The pie chart shows the relative distribution over the transcriptional classes of the bacteriophage proteins involved in bacteriophage–host interactions after exclusion of the proteins of unknown class (eight proteins). One phage protein is member of both the early and the middle (class II) proteins. *The late proteins are structural proteins that are internalized during infection and exert their effect early during infection.

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Interestingly, 90% of the phage proteins involved are smaller than 250 amino acids and many of the corresponding genes can be deleted without seriously affecting phage production under standard laboratory conditions. This suggests that these phage proteins are only necessary under specific environmental conditions, for infecting specific hosts, or have a redundancy in their function (Miller et al., 2003). The functional mechanisms of only a small fraction of these gene products are (at least partially) understood and since these proteins show little or no sequence similarity to other proteins, sequence-based predictions are largely absent. Since some bacteriophage early genes are lethal or very deleterious to the host cells, research focus has shifted primarily to the use of these bacteriophage–host interactions for the identification of new antibacterial targets (Liu et al., 2004). In contrast, the role of non-inhibitory proteins has been largely ignored, mainly due to the lack of functional indicators for these gene products.

To date, over 500 Caudovirales genomes have been sequenced. Each of these projects adds predicted genes to the immense pool of uncharacterized phage genes, most of which show no similarity to other proteins in the databases (Pedulla et al., 2003; Kwan et al., 2005; 2006). The functional characterization of these ORFans is one of the major challenges of bacteriophage molecular biology (Comeau et al., 2008). Even with the intensively studied bacteriophage T4 almost half of the predicted ORFs do not have an assigned function, a large majority of which lie in regions transcribed by the strong early promoters (Miller et al., 2003). The available genome data suggest that most phage–host interactions remain unstudied. This review attempts to outline the interaction mechanisms among the Caudovirales and place them in their functional perspective and their potential towards applications.

Mechanisms of bacteriophage–host interactions

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of bacteriophage–host interactions
  5. Bacteriophage–host interactions direct transcription in phage T4-infected cells
  6. Bacteriophage–host interactions assist transcription in phage T7-infected cells
  7. Bacteriophage–host interactions influencing replication of the host cell
  8. Do phages influence the translation apparatus?
  9. Bacteriophage–host interactions protect the phage genome from degradation
  10. Influence of bacteriophage–host interactions on proteolysis
  11. Discussion and applications
  12. References

The overview of intensely studied bacteriophage–host interactions (Table 1) clearly demonstrates the wide variety of the targeted host proteins and the mechanisms used. Apart from the most common and diverse types of bacteriophage–host interactions (their role in the regulation of transcription, the influence on host replication and alleviation of restriction of the phage genome), this review also focuses on the potential influence of bacteriophage–host interactions on translation and proteolysis, two mechanisms that are – at this time – less well documented but may prove to be more general than previously anticipated. While only some examples are provided due to space restrictions, all are listed and referenced in Table 1.

To illustrate the profound impact bacteriophages have on transcription in the infected host cell, transcription in T4- and T7-infected cells is discussed. The former is a multistage process displaying a wide variety in interactions, whereas the latter is an example of a phage protein serving multiple roles through various interactions. Some other well-studied examples of phage-directed transcription (e.g. phage λ and SPO1, see Table 1) are not discussed here but endorse the variety of bacteriophage–host interactions.

Bacteriophage–host interactions direct transcription in phage T4-infected cells

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of bacteriophage–host interactions
  5. Bacteriophage–host interactions direct transcription in phage T4-infected cells
  6. Bacteriophage–host interactions assist transcription in phage T7-infected cells
  7. Bacteriophage–host interactions influencing replication of the host cell
  8. Do phages influence the translation apparatus?
  9. Bacteriophage–host interactions protect the phage genome from degradation
  10. Influence of bacteriophage–host interactions on proteolysis
  11. Discussion and applications
  12. References

The temporal regulation of bacteriophage T4 gene expression is a complex and flexible process, which depends primarily on the sequential activation and inactivation of different promoter classes (early, middle and late). Transcription termination and antitermination also play an important role. In addition, post-transcriptional mechanisms blur the regulation of this process (Mosig and Hall, 1994).

T4 early transcription is accompanied by the shutoff of host transcription

Throughout infection, T4 relies entirely on the host RNA polymerase. At the start of infection, the T4 early promoters have to compete with host promoters for the unmodified host RNA polymerase (Fig. 2). The early phage promoters closely resemble the host σ70-dependent promoters and seem to be stronger than any bacterial promoter (Wilkens and Rüger, 1996). In addition, the internal head protein Alt efficiently ADP-ribosylates one of the two α subunits of the host RNA polymerase. Three other polymerase subunits (β, β′ and σ70) are modified to a lesser extent (Rohrer et al., 1975). Although not essential (Goff and Setzer, 1980), ADP-ribosylation by Alt increases affinity for the T4 early promoters and supports preferential transcription from T4 early promoters after infection (Fig. 2) (Koch et al., 1995; Wilkens et al., 1997). The A-rich UP element, present in most T4 early promoters, contributes to this strong interaction (Sommer et al., 2000). Both the promoter strength and the modification of the α subunit of the host RNA polymerase ensure efficient transcription of T4 early promoters, independently of the shutoff of host transcription.

image

Figure 2. Modifications of the E. coli RNA polymerase throughout different stages of bacteriophage T4 infection cycle. Filled shapes represent proteins involved in transcription (proteins are not drawn to scale). Lines represent promoter DNA. Specific sequence motifs recognized by proteins are indicated. Bacterial and viral components (proteins or DNA) are indicated in blue and red respectively. The transcription complexes at different stages of the infection cycle are shown: (A) the unmodified host RNA polymerase, (B) shutoff of host transcription, (C) early, (D) middle and (E) late transcription complex, which is coupled to T4 replication (gp45).

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Shortly after infection host transcription is shut off by binding of Alc to recognition sequences in the host DNA induces premature termination of transcription from cytosine-containing DNA. Bacteriophage transcription is protected by overall substitution of cytosine with 5-hydroxymethyl cytosine in the T4 DNA (Kashlev et al., 1993). Interaction of Alc with the β subunit is essential for the termination of transcription (Severinov et al., 1994). Both α subunits of the host RNA polymerase are modified by ModA, a second ADP-ribosyltransferase produced early during infection (Skórko et al., 1977; Tiemann et al., 1999). This modified core RNA polymerase exhibits increased efficiency of rho factor-dependent termination and reduced affinity for the host-cell σ70 factor (Wilkens and Rüger, 1994), resulting in the reduced transcription from σ70 promoters and some T4 early promoters, especially those with an UP element (Goldfarb and Palm, 1981). Modification of both α subunits of the host RNA polymerase is anticipated to stimulate late transcription (Kolesky et al., 1999) (Fig. 2).

Switch from T4 early to middle transcription

Both early proteins AsiA and MotA are required for in vivo transcription of the middle genes (Ouhammouch et al., 1995). The anti-σ factor protein AsiA has a double function. First, tight binding to σ70 (Orsini et al., 1993) induces structural rearrangements (Lambert et al., 2004; Baxter et al., 2006) and inhibits transcription from T4 early promoters and host promoters that require the −35 element for activation (Ouhammouch et al., 1995; Colland et al., 1998). Second, the remodelling of σ70 creates a docking site for MotA, the second protein necessary for transcription from T4 middle promoters (Lambert et al., 2004; Baxter et al., 2006). The AsiA-induced remodelling makes the C-terminus of σ70 available for interaction with a cleft located on the N-terminal domain of MotA (Bonocora et al., 2008). While the N-terminus of MotA is required to activate transcription (Finnin et al., 1997), the C-terminus binds to the MotA box (TGCTT) (Pande et al., 2002), a motif centred at −30 in T4 middle promoters (Marshall et al., 1999). Therefore, MotA serves as a molecular bridge between σ70 and the DNA, and functionally substitutes for the interaction of σ70 with its −35 DNA element, without influencing the σ70-mediated recognition of the −10 element (Fig. 2) (Pande et al., 2002).

T4 late transcription is dependent on T4 genome replication

In contrast to transcription from T4 early and middle promoters, late transcription is independent of the host σ70. A T4-encoded σ factor (gp55) mediates recognition of T4 late promoters by the host RNA polymerase (Kassavetis et al., 1983), which are characterized by an 8 bp motif (TATAAATA) centred 10 bp upstream of transcription start site (Christensen and Young, 1982). Although gp55 is sufficient for accurate transcription initiation (Kassavetis et al., 1983), efficient transcription of late genes requires co-activator gp33 and DNA-loaded sliding clamp gp45. Gp55 and gp33 interact with the host RNA polymerase core at sites that are the principal attachment points of the host σ70 (Wong et al., 2003; Nechaev et al., 2004). However, the trimeric gp45 does not interact directly with the core RNA polymerase but tracks along the T4 DNA and through interaction with the C-termini of gp33 and gp55 stimulates transcription from the T4 late promoters (Fig. 2) (Herendeen et al., 1992).

Although gp45 interacts with both gp55 and gp33, the loss of interaction between gp33 and gp45 abolishes efficient transcription elongation (Nechaev and Geiduschek, 2008). In addition, gp33 strongly inhibits basal transcription by the gp55–RNA polymerase complex in the absence of gp45 (Nechaev and Geiduschek, 2006). Through this dual function, gp33 ensures complete dependence of T4 late transcription on the presence of DNA-loaded gp45 without taking part in promoter recognition (Herendeen et al., 1992). Remarkably, gp45 also functions as a DNA-loaded sliding clamp in the T4 DNA replication complex, enhancing the processivity of this complex (Mace and Alberts, 1984). Since gp45 is loaded on DNA at the primer–template junction of the replication fork (Capson et al., 1991; Munn and Alberts, 1991), only replicating phage DNA can support T4 late transcription (Wiberg et al., 1962).

Transcription from late promoters outcompetes middle transcription, especially when both RNA polymerase subunits are ADP-ribosylated (by ModA) and RpbA is bound to the RNA polymerase core (Fig. 2) (Hsu et al., 1987; Kolesky et al., 1999). RpbA is produced throughout the early and middle stages of infection (Hsu and Karam, 1990). In addition, the involvement of other unknown effectors is anticipated (Kolesky et al., 1999).

Other bacteriophage–host interactions influencing T4 transcription

At least three other bacteriophage–host interactions are suggested to play a role in the regulation of T4 transcription. Phosphorylation of the heat shock sigma factor σ32 is downregulated by T4 proteins Mrh and Srh. In addition, Srh shows sequence similarity to a segment of σ32, which is responsible for the interaction of σ32 with the RNA polymerase core enzyme (Frazier and Mosig, 1990; Mosig et al., 1998). This suggests T4 could influence competition of σ32 for the core polymerase. Such a mechanism could favour the binding of T4 gp55 to the RNA polymerase and therefore take part in regulation of T4 late transcription. T4 protein Srd also resembles the RNA polymerase core interaction domain of σ70 and σ38 (stationary-phase and oxidative stress sigma factor), suggesting Srd could also act as a decoy for these transcription factors (Frazier and Mosig, 1990; Mosig et al., 1998).

Bacteriophage–host interactions assist transcription in phage T7-infected cells

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of bacteriophage–host interactions
  5. Bacteriophage–host interactions direct transcription in phage T4-infected cells
  6. Bacteriophage–host interactions assist transcription in phage T7-infected cells
  7. Bacteriophage–host interactions influencing replication of the host cell
  8. Do phages influence the translation apparatus?
  9. Bacteriophage–host interactions protect the phage genome from degradation
  10. Influence of bacteriophage–host interactions on proteolysis
  11. Discussion and applications
  12. References

Bacteriophage T7 transcription is coupled to genome internalization. The first 850 bp on the left end of the genome enter the cell at a constant rate (Kemp et al., 2004). Subsequently, the Escherichia coli RNA polymerase initiates transcription of the early genes from one or more of the three strong σ70-dependent promoters located on the 850 bp already translocated into the cell (Zavriev and Shemyakin, 1982). By tracking along the T7 genome, the transcribing host RNA polymerase pulls at least 7 kb of the T7 genome into the infected cell (Zavriev and Shemyakin, 1982).

Regulation of phage T7 early transcription

Among the early proteins produced are gp0.7 and the phage-encoded RNA polymerase (gp1) (Chamberlin et al., 1970). Gp0.7 has two physically separable activities and influences transcription in T7-infected cells in several ways (Fig. 3). While the C-terminal domain participates directly in host transcription shutoff, the N-terminal part carries a protein kinase domain (Rahmsdorf et al., 1974; Michalewicz and Nicholson, 1992). Gp0.7 phosphorylates over 90 host proteins including the β′ subunit of the host RNA polymerase, RNase III, RNase E and RhlB. These targets function in transcription and related processes. The importance of phosphorylation of the host proteins involved in translation is discussed later (Robertson and Nicholson, 1990; 1992; Robertson et al., 1994).

image

Figure 3. Overview of the various functions of T7 gp0.7. Gp0.7 consists of two domains: the N-terminal protein kinase domain and the C-terminal domain that act independently. Details about the illustrated processes are discussed in the text. (A) Improved discrimination between T7 early and middle transcription, (B) shutoff of T7 early and host transcription, (C) increased processing of T7 mRNA by RNase III, (D) protection of T7 middle and late mRNA from degradosome-mediated degradation, (E) the possible influence on the translation apparatus (30S and 50S ribosomal subunits).

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The early region of the T7 genome is delineated by a transcription terminator (Studier, 1972); however, efficient termination is depending on phosphorylation of the β′ subunit of the host RNA polymerase. Gp0.7 confers increased transcription termination, improving discrimination between T7 early to middle gene expression by phosphorylation of the β′ subunit of the host RNA polymerase (Fig. 3A) (Zillig et al., 1975; Pfennig-Yeh et al., 1978; Severinova and Severinov, 2006).

The shift to T7 middle transcription is accompanied by host transcription shutoff

About 6 min after infection at 30°C, the phage-encoded RNA polymerase starts transcription of the middle genes and translocates the remainder of the T7 genome into the cell (García and Molineux, 1995). Soon after the onset of middle transcription (8 min post infection at 30°C), T7 early transcription along with host transcription is shut off (Studier, 1972). Viral proteins gp0.7 (early protein) and gp2 (middle protein) are implicated in this process. The C-terminal domain of gp0.7 inhibits the host-catalysed transcription (Michalewicz and Nicholson, 1992). However, the mechanism and the possible interaction site on the host RNA polymerase remain uncharacterized (Fig. 3B).

Gp2, one of the first middle proteins produced, binds the E. coli RNA polymerase and inhibits host-dependent transcription (Hesselbach and Nakada, 1975; 1977). Interaction with the β′ subunit prevents promoter recognition by the σ70 holoenzyme but upon formation of an open promoter complex gp2 can no longer bind its target. Gp2 prevents σ from binding to the −35 promoter region (Nechaev and Severinov, 1999). This protein's ability to inhibit host RNA polymerase activity is essential for infection by T7. Interestingly, gp2 also indirectly contributes to DNA packaging since amber mutants in gene 2 are packed less efficiently (LeClerc and Richardson, 1979). During packaging of the concatemeric T7 genome, T7 RNA polymerase is hypothesized to pause at the genome-end junctions and recruits the terminase complex responsible for packaging. Since the transcription elongation rate of the host RNA polymerase is much lower than that of the T7 RNA polymerase, it probably stalls the viral polymerase inducing aberrant pausing and packaging (Qimron et al., 2008).

Influence on viral mRNA processing and stability

The T7 mRNA processing, involving cleavage by RNase III, is required for the efficient translation of some early proteins (Dunn and Studier, 1975; Saito and Richardson, 1981). RNase III activity is stimulated fourfold after phosphorylation by gp0.7, presumably enhancing stability and maturation of T7 mRNA (Fig. 2C) (Mayer and Schweiger, 1983).

Transcription by the bacteriophage-encoded RNA polymerase is more than fivefold faster at 200–300 bases per second (at 30°C) than transcription by the host RNA polymerase (Golomb and Chamberlin, 1974), thus outpacing translating ribosomes bound to the viral mRNA (Iost et al., 1992). As a consequence, long stretches of naked mRNA are created behind the T7 RNA polymerase (Marchand et al., 2001). In the absence of gp0.7 protein kinase activity, these mRNAs are more sensitive to degradation by the degradosomes than their counterparts synthesized by the E. coli RNA polymerase. The degradosomes consists of RNase E, enolase, polynucleotide phosphorylase and ATP-dependent RNA helicase RhlB (Iost and Dreyfus, 1995; Py et al., 1996). Gp0.7-mediated phosphorylation of RNase E and RhlB inhibits degradosome-mediated degradation of naked mRNA but no other RNase E activities. Hence, gp0.7 is instrumental to the stabilization of T7 middle and late mRNA molecules and this again illustrates the multiple helper role of gp0.7 in bacteriophage T7 infection (Fig. 3D) (Marchand et al., 2001).

Bacteriophage–host interactions influencing replication of the host cell

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of bacteriophage–host interactions
  5. Bacteriophage–host interactions direct transcription in phage T4-infected cells
  6. Bacteriophage–host interactions assist transcription in phage T7-infected cells
  7. Bacteriophage–host interactions influencing replication of the host cell
  8. Do phages influence the translation apparatus?
  9. Bacteriophage–host interactions protect the phage genome from degradation
  10. Influence of bacteriophage–host interactions on proteolysis
  11. Discussion and applications
  12. References

Although not as common as targeting the transcription machinery, increasing evidence shows that some phages also directly target the host replication machinery. While many lytic phages encode most of the proteins for their genome replication, temperate phages as well as some lytic phages depend heavily upon the host replication machinery (Friedman et al., 1984). Through bacteriophage–host interactions, host proteins are recruited for the replication of the bacteriophage genome, often causing the abolition of host replication. So far, there is no evidence that inhibition of host genome replication is strictly necessary for phage infection. In addition, before replication of the phage genome the host nucleoid is often degraded to provide precursors for phage replication (Guttman et al., 2005). Since the bacteriophage–host interactions involved in replication of the λ genome have been studied in most detail they are discussed here. Of special interest are seven other bacteriophage–host interactions recently discovered by Liu and colleagues (2004) because they show interference with host replication does not act through a single target.

Replication of the phage λ genome depends on the interaction of λ protein P (λ P) with the E. coli DnaB, the replicative DNA helicase (Klein et al., 1980). In a first phase, the λ initiation protein O (λ O) binds to the λori forming a large nucleoprotein structure. Subsequently, λ P recruits DnaB to this structure by direct interaction with λ O (Dodson et al., 1985). λ P competes efficiently with the E. coli helicase loader for DnaB. The interaction of λ P with DnaB strongly inhibits the ATPase activity of the helicase as well as its ability to assist the E. coli primase, blocking E. coli replication (Mallory et al., 1990). Transformation of DnaB into a processive helicase at the λori requires removal of λ P from this complex by E. coli DnaK, DnaJ and GrpE heat shock proteins. In the final stage, the other components of the replication machinery assemble spontaneously (Zylicz et al., 1989). Although employing a different replication strategy, temperate bacteriophage P2 also encodes a protein (protein B) for loading DnaB onto the phage origin of replication (Odegrip et al., 2000).

An analysis of 27 Staphylococcus aureus phages revealed seven different phage protein families that target and inhibit the replication machinery of the host cell. Four S. aureus proteins are targeted: the helicase loader, primase, β subunit of DNA polymerase III (the sliding clamp) and an uncharacterized replication protein (Liu et al., 2004). Except for phage Twort gp168 and phage G1 gp240, the mechanisms of these interactions have not been studied. Both these proteins interact with the β subunit of DNA polymerase III (Belley et al., 2006), which functions as a sliding clamp increasing the processivity and incorporation rate of DNA replication (O'Donnell et al., 1992). After loading of the sliding clamp on single-stranded DNA by the clamp loader (Jeruzalmi et al., 2001), the replicative DNA polymerase binds to the sliding clamp resulting in rapid and processive replication of the bacterial genome (López de Saro et al., 2003). By interacting with the sliding clamp, Twort gp168 and G1 gp240 efficiently compete with the clamp loader and the replicative DNA polymerase. Thereby, they prevent both loading onto DNA and the interaction with the replicative polymerase (Belley et al., 2006). The involvement of these proteins in phage genome replication remains to be studied.

Do phages influence the translation apparatus?

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of bacteriophage–host interactions
  5. Bacteriophage–host interactions direct transcription in phage T4-infected cells
  6. Bacteriophage–host interactions assist transcription in phage T7-infected cells
  7. Bacteriophage–host interactions influencing replication of the host cell
  8. Do phages influence the translation apparatus?
  9. Bacteriophage–host interactions protect the phage genome from degradation
  10. Influence of bacteriophage–host interactions on proteolysis
  11. Discussion and applications
  12. References

Bacteriophages are also dependent on the translation apparatus of the host cell. Apart from influencing mRNA stability and processing (discussed above), several lines of evidence suggest a direct influence of bacteriophage infection on translation. Both bacteriophage T4 and T7 modify proteins which are directly involved in translation. Until now their mechanisms as well as their outcome remain elusive. Regulation of gene expression of φYS40 seems to be controlled – at least in part – by influencing translation. Although the exact mechanism governing this regulation is not known yet, this example shows regulation of translation is a relevant theme in phage biology. Apart from providing an overview of the scarce data available (direct interactions have only been shown for bacteriophage T4 and T7), this section aims at drawing attention to these largely ignored interactions.

Several proteins involved in translation are ribosylated during T4 infection (Table 2). Bacteriophage T4 encodes three ADP-ribosyltransferases: Alt, ModA and ModB. ModA, however, functions exclusively in regulation of transcription (Goldfarb and Palm, 1981). Alt and ModB modify 27 and 8 proteins, respectively, some of which are directly involved in translation (Depping et al., 2005) (Table 2). However, the individual effects of these modifications are unknown. These modifications suggest a discriminating or non-discriminating influence on the translation process during T4 infection. Translation initiation, elongation and also peptide maturation are possibly affected (Depping et al., 2005).

Table 2.  Bacteriophage T7 gp0.7 and bacteriophage T4 Alt and ModB target host proteins involved in translation.
Phage proteinHost targetFunction
T7 gp0.7Initiation factor IF1aHelper function for IF2 and IF3b
Initiation factor IF2aBinding and functional commitment of fMet-mRNAb
Initiation factors IF3aSelection of the mRNA translation initiation regions ribosome dissociationb
Elongation factor GaFacilitate translocationb
Elongation factor Pa,dStimulates the peptidyltransferase activityb
30S ribosomal subunit S1aS1 promotes binding of mRNA that is otherwise inefficiently recognizedb
30S ribosomal subunit S6aS6 is a 16S rRNA-binding proteinb
T4 AltProlyl-tRNA synthetasecSynthesizes prolyl-tRNAb
Elongation factor EF-TucBinds and recruits aminoacyl-tRNAsb
Trigger factorcChaperone interacting with the nascent peptide chainb,e
T4 ModBElongation factor EF-TucBinds and recruits aminoacyl-tRNAsb
30S ribosomal subunit S1cS1 promotes binding of mRNA that is otherwise inefficiently recognizedb
Trigger factorcInteracting with the nascent peptides chainb

As discussed earlier bacteriophage T7 protein kinase (gp0.7) phosphorylates over 90 proteins during infection (Robertson et al., 1994). Seven targets of gp0.7 identified so far are directly involved in translation (Table 2). Phosphorylation of these proteins coincides with the onset of T7 late protein synthesis (Robertson and Nicholson, 1992; Robertson et al., 1994). Their modification suggests an influence on both translation initiation, which is rate limiting, and translation elongation (Robertson et al., 1994). Although the individual effects of these modifications are unknown, Yamada and co-workers described a stimulation of in vitro translational activity of ribosomes from T7-infected cells, but no specific activity towards late mRNA molecules was observed (Yamada and Nakada, 1976). Protein kinase activity of gp0.7 also stimulates late mRNA translation (Robertson and Nicholson, 1992). In addition, a shift from the 70S ribosome to the separate 30S and 50S subunits was noticed, suggesting increased initiation (Strome and Young, 1980). On the whole these results suggest a non-discriminating influence on both translation initiation and elongation during phage T7 infection (Fig. 3E) (Robertson and Nicholson, 1992).

Although not directly involving bacteriophage–host interactions so far, a recent study of regulation of Thermus thermophilus bacteriophage φYS40 gene expression also suggests targeting of translation. During infection there is a significant increase and decrease in transcription of IF2 and IF3 respectively (Sevostyanova et al., 2007). An increased concentration of IF2, combined with a low concentration of IF3, stimulates translation initiation of leaderless transcripts (Tedin et al., 1999; Grill et al., 2001). Along with the observation that most middle and late phage transcripts are leaderless, this finding suggests that φYS40 gene expression might be controlled at the level of translation instead of transcription (Sevostyanova et al., 2007). Such an influence on translation is discriminating, i.e. there is a preference for translation of bacteriophage mRNA over host mRNA.

Bacteriophage–host interactions protect the phage genome from degradation

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of bacteriophage–host interactions
  5. Bacteriophage–host interactions direct transcription in phage T4-infected cells
  6. Bacteriophage–host interactions assist transcription in phage T7-infected cells
  7. Bacteriophage–host interactions influencing replication of the host cell
  8. Do phages influence the translation apparatus?
  9. Bacteriophage–host interactions protect the phage genome from degradation
  10. Influence of bacteriophage–host interactions on proteolysis
  11. Discussion and applications
  12. References

Restriction-modification systems protect the bacteria from bacteriophage as well as other foreign DNAs entering the cell (Bertani and Weigle, 1953; Arber, 1979). Typically, restriction-modification systems consist of two enzymatic functions responsible for opposite activities: a restriction endonuclease that cleaves a specific DNA sequence and a methyltransferase that confers protection from cleavage by modifying bases within the same DNA sequence. While the bacterial genome is protected from degradation by methylation of adenine or cytosine bases within the recognition sequence, the unmodified foreign DNA is inactivated by endonucleolytic cleavage (Boyer, 1971; McClelland, 1981; Yuan, 1981). Bacteriophages have developed a variety of different mechanisms to escape restriction in the host cell (Krüger and Bickle, 1983). This illustrate the evolutionary arms race between bacteria and bacteriophages (Tock and Dryden, 2005).

At least five different antirestriction strategies are employed by bacteriophages: DNA sequence alteration, occlusion of restriction sites, stimulation of methylation of the incoming phage DNA by host factors, degradation of cofactors, incorporation of hypermodified bases in the phage DNA (or modification of the DNA after replication) and direct inhibition of restriction-modification enzymes (Krüger and Bickle, 1983; Tock and Dryden, 2005). So far, only two protection mechanisms have been shown directly to involve bacteriophage–host interactions: the direct inhibition of restriction-modification enzymes and the incorporation of hypermodified bases in the phage DNA (Warren, 1980). While direct inhibition of restriction activity always involves the interaction with a phage protein, there are many examples of incorporation of unusual bases in the phage DNA or modification of the bases after replication that do not depend on bacteriophage–host interactions (Krüger and Bickle, 1983; Tock and Dryden, 2005). A third mechanism, the stimulation of methylation of the phage genome, has been hypothesized to involve bacteriophage–host interactions. For all three mechanisms examples are discussed in the following paragraphs. In addition, an overview of the antirestriction systems of bacteriophage T4 is provided to illustrate the variety in these interactions, even within a single phage.

Direct inhibition of restriction-modification enzymes

Ocr (Overcome classical restriction, gp0.3), the first T7 protein produced after infection (Studier, 1973), interacts directly with Type I restriction endonucleases by blocking their DNA binding site. As such, it inhibits Type I restriction endonucleases protecting the viral genome from degradation which in turn enables the phage to propagate (Bandyopadhyay et al., 1985). The Ocr homodimer mimics the size, shape and charge of 24 bp double-stranded bent B-form DNA. Since the affinity of the Type I restriction enzyme EcoKI for Ocr is at least 50-fold higher than for DNA, Ocr competes efficiently with DNA for binding to the specificity unit of the restriction enzyme. As a consequence, the binding of Ocr inhibits restriction as well as modification (Walkinshaw et al., 2002). Recently, phage λ protein Gam was also found to mimic DNA. Gam inhibits RecBCD nuclease and helicase activity, although the exact mechanism is not fully understood. In contrast to other inhibitors of restriction-modification enzymes, Gam specifically protects viral DNA during replication (Court et al., 2007).

The bacteriophage T4 DNA is heavily modified: hydroxymethylcytosine (HMC) instead of cytosine is incorporated during replication, after replication HMC residues are variably glucosylated. In addition, the adenosine residues within the DNA are methylated (Carlson et al., 1994). Even though the T4 genome is heavily modified, the bacteriophage also encodes several restriction endonuclease inhibitors. While HMC-containing DNA is protected from classical restriction-modification systems, Mcr restriction systems are specific for DNA with modified cytosines. The ability to glucosylate the hydroxymethyl groups provides protection from Mcr-directed restriction (Bickle and Krüger, 1993). However, the T4 gene product Arn probably protects the unglucosylated T4 genome from degradation (Dharmalingam et al., 1982) by direct interaction with RglB (Carlson et al., 1994). Another modification-dependent restriction endonuclease, GmrSD, specifically targets and cleaves glucosylated HMC-containing DNA. T4 protein IPI*, an internal head protein injected along with the genome into the host cell, protects the modified DNA from GmrSD restriction (Bair et al., 2007). This protein inhibits GmrSD through a direct protein–protein interaction. Recently, GmrSD-related restriction enzymes insensitive to IPI* inhibition have been identified (Rifat et al., 2008). This highlights a new step in an intense co-evolution of bacterial defence mechanisms and bacteriophage attack strategies.

A role for bacteriophage–host interactions in incorporation of unusual bases in phage DNA

Bacteriophage–host interactions can also indirectly protect phage DNA from restriction. Incorporation of uracil instead of thymine protects the genome of Bacillus subtilis phages PBS1 and PBS2 from degradation (Takahashi and Marmur, 1963). Normally, incorporation of uracil in DNA is counteracted by the host-encoded uracil-DNA glycosylase, which removes uracil bases from the DNA. PBS1 and PBS2 encode Ugi, an inhibitor of the uracil-DNA glycosylase (Wang and Mosbaugh, 1989). By mimicking the uracil-containing double-stranded DNA, Ugi interacts with the uracil-DNA glycosylase trapping it in an irreversible state. Similarly to Ocr, the carboxylate groups of aspartate and glutamate imitate the position of the phosphate backbone of double-stranded DNA (Putnam et al., 1999). The structure of Ocr, Ugi and Gam suggest DNA mimicry to alleviate destruction of the bacteriophage genome is a common theme among phages.

Stimulation of methylation of the bacteriophage genome

λ protein Ral (restriction alleviation) alleviates restriction and enhances methylation by the E. coli K-12 restriction-modification system EcoKI, which is encoded by hsdR, hsdM and hsdS (Zabeau et al., 1980), whereas under normal conditions, the unmodified (bacteriophage) DNA is a good substrate for restriction and the hemimethylated DNA is fully modified (Powell et al., 1993). Since Ral also enhances modification in the absence of the HsdR subunit, Ral is hypothesized to exert its effect through an interaction with HsdM or/and HsdS. However, the molecular mechanism of this bacteriophage–host interaction remains to be elucidated (Loenen and Murray, 1986).

Influence of bacteriophage–host interactions on proteolysis

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of bacteriophage–host interactions
  5. Bacteriophage–host interactions direct transcription in phage T4-infected cells
  6. Bacteriophage–host interactions assist transcription in phage T7-infected cells
  7. Bacteriophage–host interactions influencing replication of the host cell
  8. Do phages influence the translation apparatus?
  9. Bacteriophage–host interactions protect the phage genome from degradation
  10. Influence of bacteriophage–host interactions on proteolysis
  11. Discussion and applications
  12. References

Apart from influencing transcription or translation, influencing proteolysis might serve as an additional mechanism for regulating or fine tuning the proteome of the infected cell. However, not much is known about bacteriophage–host interactions influencing proteases. So far, two bacteriophage–host interactions directed against host-encoded proteases are known: λ protein CIII and T4 protein PinA inhibit FtsH and Lon respectively. Future research towards these interactions will have to show whether these are isolated examples or that these mechanisms are more common.

By binding to and inhibiting FtsH, λ CIII leads to an increase in the levels of the λ CII transcriptional activator, which is the key regulator of the lysis-lysogeny decision (Oppenheim et al., 2005). CIII adopts an oligomeric structure and functions as a competitive inhibitor by preventing binding of CII to FtsH. At the same time, CIII is subjected to proteolysis by FtsH, which limits the activity of this bacteriostatic protein to a short time window and allows for its rapid elimination once lysogeny has been established (Kobiler et al., 2007). The T4 early protein PinA binds as a dimer to Lon with high affinity. It inhibits the ATP-dependent protease activity of Lon by blocking the coupling between ATP hydrolysis and peptide bond cleavage (Hilliard et al., 1998a,b). As a result, T4 proteins might be stabilized in T4-infected E. coli cells by reducing their turnover. However, PinA has no influence on the turnover of stable E. coli proteins.

Discussion and applications

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of bacteriophage–host interactions
  5. Bacteriophage–host interactions direct transcription in phage T4-infected cells
  6. Bacteriophage–host interactions assist transcription in phage T7-infected cells
  7. Bacteriophage–host interactions influencing replication of the host cell
  8. Do phages influence the translation apparatus?
  9. Bacteriophage–host interactions protect the phage genome from degradation
  10. Influence of bacteriophage–host interactions on proteolysis
  11. Discussion and applications
  12. References

As illustrated in the previous sections and Table 1, bacteriophages influence the host machinery and metabolism using a variety of modes. The limited number of thoroughly characterized bacteriophage–host interactions creates the impression that these interactions are isolated cases. However, combined evidence suggests that these bacteriophage–host interactions are a common theme in the Caudovirales and possibly in all bacterial and archeal viruses. Due to the limited number of systematically identified interactions, a full comparison of the repertoire of interactions of different phage types, e.g. virulent versus temperate, is not straightforward. At this point, there are no indications that interactions of temperate phages would be less ‘aggressive’ than virulent phages. For instance, bacteriophage λ has several genes, the expression of which is deleterious to E. coli. However, these interactions are inactive during lysogeny. More likely, a part of the repertoire of bacteriophage–host interactions of a particular phage type is dependent on the machinery encoded by that phage. For instance, phages devoid of their own replication machinery use bacteriophage–host interactions to efficiently engage the host's system.

Together with the absence of functional indications, the low or often complete absence of sequence similarity seriously hampers functional characterization of the proteins. We recently proposed a yeast two-hybrid-based procedure for the systematic identification of phage–host interactions revealing non-inhibitory bacteriophage–host interactions for Pseudomonas aeruginosa Podovirus φKMV (Roucourt et al., 2009). Screening 10 φKMV early proteins identified five completely new types of bacteriophage–host interactions: an enzyme of the central energy metabolism, a regulator of a secretion system, a regulator of nitrogen metabolism, a chaperone helper protein and a membrane protein. This study also indicates the complexity and subtle nature of bacteriophage–host interactions (Roucourt et al., 2009; K. Hertveldt, unpubl. results). In an alternative approach, Westblade and co-workers identified the bacteriophage proteins targeting the host RNA polymerase using affinity purification of this tagged complex. Although this approach is focused to a single host protein, it allows investigation of all phages infecting that particular host strain (Savalia et al., 2008; Westblade et al., 2008). This method enables high-throughput identification of phage proteins directed towards a particular host protein, whereas our yeast two-hybrid approach allows screening of a phage protein against all proteins of a particular host. Although it does not provide clear-cut answers the elucidation of the bacteriophage–host interactome will help to elucidate the function of the early phage proteins. In addition, this approach will show which phage and host strain mutants could provide further information on the function of the phage protein or which other experiments are relevant.

Even though the number of characterized bacteriophage–host interactions is limited, some general hypotheses can be made about these interactions and the corresponding bacteriophage early proteins.

  • • 
    Bacteriophage–host interactions are probably very common and are often directed by early and small bacteriophage proteins.
  • • 
    Most bacteriophage–host interactions are probably not essential for host infection, but can have an influence on the infection efficiency.
  • • 
    A substantial fraction of the interactions are only needed under specific conditions or for efficient infection of specific hosts.
  • • 
    The bacteriophage–host interactions possessed by a particular phage are probably dependent on its ecological niche.
  • • 
    Through their interaction bacteriophage early proteins inhibit or stimulate the function of the targeted host protein or redirect the protein to a role in the infection cycle not related to its function.
  • • 
    While a limited number of early bacteriophage genes are observably toxic to the host, a large group is probably not deleterious upon expression.

Apart from its fundamental importance to phage biology, elucidation of the function of bacteriophage–host interactions is of importance for potential applications like phage therapy. The acceptance of phage therapy at the regulatory and legislative level may become dependent on a solid background concerning the molecular capabilities of these entities. In addition, bacteriophage–host interactions also have direct and specific applications.

The identification of toxic bacteriophage products and their interaction partners have been used for the identification of new antibacterial targets. Liu and co-workers applied the concept of phage protein-mediated growth inhibition to develop new antibacterial compounds against S. aureus, based on the protein–protein interaction between phage and bacterium (Liu et al., 2004). Out of 964 ORFs originating from 27 S. aureus phages Liu and co-workers identified 31 novel phage proteins exerting a growth inhibitory effect on this bacterium. The bacteriophage–host interaction-based growth inhibitory proteins represent only a small fraction (3.2%) of the proteins tested. Based on one of these bacteriophage–host interactions, small molecules mimicking the growth inhibitory effect of phage proteins were developed. This experiment validates the premises of mimicking the growth-inhibitory effect of phage proteins by a chemical compound (Liu et al., 2004). This interaction-based approach for the development of antibacterial molecules overcomes several difficulties. The targets have been selected and evolutionary validated to be susceptible to inhibition, while being essential to the host. At the same time, inhibition by a bacteriophage protein shows that the targets are accessible to other molecules. The universality of the screening assay overcomes possible difficulties related to the development of a suitable screening assay for a target. In addition, it facilitates screening of multiple targets (Brown, 2004; Liu et al., 2004; Projan, 2004).

The novel types of non-inhibitory bacteriophage–host interactions identified for bacteriophage φKMV (Roucourt et al., 2009; K. Hertveldt, unpublished), along with the diversity in known targets and the high number of uncharacterized phage early genes, suggest that bacteriophages target a wide variety of processes in the host cell, many of them non-essential. Of course, one particular bacteriophage only has a limited number of bacteriophage–host interactions tailored to the needs of the ecological niche in which the phage infects its host cells. From an application perspective, one may envision a collection of bacteriophage genes as a source of proteins controlling and redirecting various aspects of the bacterial metabolism and machinery. As a consequence, various potential applications may lie outside the search for antibacterial targets, in broader fields including biotechnological tools and systems biology. Indeed, both toxic and, perhaps especially, non-toxic phage–host interactions may hold the key for specifically controlled metabolic manipulation of bacteria. As such, numerous bioindustrial applications can be envisioned, ranging from steering mechanisms in bacterial fermentation in the food and the biotechnology industry to modifications of probiotic or therapeutic bacteria. At the same time, such research can provide critical information in the elucidation of metabolic processes in pathogenic bacteria. Considering the crucial role bacteriophages have played in the development of molecular biotechnological research over the last decades, we can hypothesize that these interactions may very well prove to be critical in the future development of this research domain. Finding proteins directed towards specific processes is probably dependent on the availability of phages from environments in which these processes are of relevance to the host cell. In addition, to find the proteins of interest in this immense unexplored gene pool, powerful and accurate screening assays are crucial. As molecular biology enters the post-genomic era, many new techniques are available in the field of transcriptomics, proteomics, interactomics and metabolomics for unravelling these puzzling interactions. In addition, metagenomics, in combination with the infection efficiency on different host strains, will provide hints for those bacteriophage early proteins needed for infection of particular host strains.

References

  1. Top of page
  2. Summary
  3. Introduction
  4. Mechanisms of bacteriophage–host interactions
  5. Bacteriophage–host interactions direct transcription in phage T4-infected cells
  6. Bacteriophage–host interactions assist transcription in phage T7-infected cells
  7. Bacteriophage–host interactions influencing replication of the host cell
  8. Do phages influence the translation apparatus?
  9. Bacteriophage–host interactions protect the phage genome from degradation
  10. Influence of bacteriophage–host interactions on proteolysis
  11. Discussion and applications
  12. References