Bacteriophages: Their Structural Organisation and Function

3.1 X-ray crystallography

X-ray crystallography was the first method used to study proteins at the atomic level, which is essential to reveal protein-ligand interactions that can boost or suppress protein activity. It is based on the principles of beam scattering within a crystal. By using specific software packages, a 3D electron density map of the protein that forms the crystal can be calculated [16]. However, to produce protein crystals, we need solutions of a protein at high concentration. The proteins have to be stable, and often mutations are made to remove their flexible parts, but this may produce different conformations to those that are required for their natural activity.

X-ray analysis is an efficient tool for analysis of protein complexes from a few kDa to hundreds of kDa in size. In order to study the structure of a large protein or a complex of several proteins, the process of crystallisation becomes a more challenging step. The development of cryoprotection in X-ray crystallography, where the crystals are flash frozen, has improved the quality of the data and often resulted in higher resolution. Nowadays, many structures of large protein complexes (up to 2–3 MDa) have been determined by X-ray analysis, but these projects have required decades to obtain high-quality crystals [17].

Viruses are much bigger particles and often have flexible components. The large size of the complexes results in significantly bigger unit cells, which results in technical challenges in obtaining fine structural details. Viruses with a rigid icosahedral lattice of the capsid have been studied successfully by X-ray crystallography at near-atomic resolution. The first viral structure was that of the Blue tongue virus (700 Å diameter) determined at a resolution of 3.5 Å which was the largest virus structure determined at that time [18]. The capsid of the Siphoviridae phage HK97 (without a portal protein) was determined at a resolution of 3.5 Å [19]. Later studies have shown that the fold of the HK97 phage capsid protein, which forms the envelope to protect viral genome from the harsh outer environment, represents a conservative fold found nowadays in nearly all dsDNA viruses so far studied.

3.2 Nuclear magnetic resonance

Nuclear magnetic resonance (NMR) is an important technique that resolves structures of small proteins that are not suitable for crystallisation due to their flexibility. This method is based on exploiting the electrical charges and spins of the nuclei in a molecule. If an external magnetic field is applied, energy is transferred to the nuclei changing their state from the level of base energy to a higher energy. This energy is emitted when the spin returns back to its base level at a frequency corresponding to radio frequencies¹. The signal that matches this transfer is measured and processed in order to yield a NMR spectrum [17, 20]. This technique is typically used for proteins of less than 200 amino acids and an upper weight limit of about 50 kDa, so it is unsuitable for the structural determination of complete viruses. However, it can be used to analyse flexibility of bigger complexes [21]. The NMR structures can be docked into low-resolution cryo-EM structures.

3.3 Electron microscopy

Light microscopy has been used for several centuries to study objects that are hardly visible to the naked eye. In conventional microscopy, resolution is mostly restricted according to the theoretical context of the Rayleigh criterion [22]. This limit is defined by the diffraction properties of light in lenses and has restricted our view to objects bigger than 250 nm. New developments in technology and advances in optical quality, electronics and software have delivered new options and extended the field of applications for electron microscopes allowing visualisation of single molecules. Electron microscopes use a beam of electrons (wavelength of less than 0.1 nm) instead of visible light (wavelength 400–700 nm). Due to their charge, the electrons can be focused using an electromagnetic field, which is why the optical system of the electron microscope (EM) is similar to the general optical system of light [23]. The short wavelength of the electron beam allows details of small objects less than 0.1 nm in size to be seen. However, biological samples are not stable in the vacuum necessary to create an image using electrons that would otherwise become absorbed by air, and, moreover, biological samples are sensitive to the electron irradiation. These factors reduce the level of achievable resolution.

At the very beginning of EM evolvement, a method called negative staining was used for visualisation of biological complexes. In this case a drop of biocomplex solution is placed on a support grid and embedded in a heavy atom salt, usually uranyl acetate [24]. Since the specific density of the negative stain is much higher than the density of the biological molecules in the microscope, we can see the cast of the molecule merged into the surrounding stain. Where the stain did not penetrate into the molecule, one can see light spots in the image as the stain has blocked electrons. Sample preparation is fast and produces very high contrast. However, this technique does not allow fine details to be seen, and the particle becomes distorted due to the drying procedure required. The stain has a relatively large grain (up to 1.5 nm) that obscures details of the molecules under study.

Nearly four decades ago, a cryo-technique for sample preparation was introduced that allows biocomplexes to be kept at nearly native conditions. A thin layer of sample on a grid is flash frozen at liquid nitrogen temperatures, thus trapping molecules in a native, hydrated state within a thin layer of amorphous ice [25]. This technique is used to study the structural organisation of biocomplexes by cryo-electron microscopy (cryo-EM) or electron tomography (cryo-ET). Until two decades ago, all data in EM was collected on films that had to be developed and digitised, which was time-consuming. The advent of charge-coupled devices (CCDs) allowed direct digital acquisition of images and the collection of large numbers of particles giving rise to structures of higher resolution. Later, direct electron detectors were introduced into EM and are now used in all high-end electron microscopes [26]. Together with new approaches in microtechnology and the automation of data collection, the results from image analysis have improved tremendously. Cryo-EM is now approaching the near-atomic resolution that had only been achieved by X-ray crystallography. New maps obtained by cryo-EM provide information on the main polypeptide chains and often reveal the positions of side chains. The current highest resolution of structures currently deposited in the EMDB is 1.5 Å [27], with many others at a resolution between 3.5 and 4 Å. At this resolution atomic models can be built and refined using the crystallographic methods.

In cryo-ET the samples are also flash frozen, but data is collected by tilting the grid with the sample between −60 and 60° around the horizontal axis (perpendicular to the optical axis of the microscope) with an increment typically of 2°. The 2D images taken at each angle are combined to calculate a 3D map of the object. The limitation in the range of the tilt results in a cone of missing data [28]. The resolution in structures obtained by cryo-ET is lower than that in single-particle analysis. However, this approach allows visualisation of important organelles within cells. If there are multiple small structures such as ribosomes or viruses, then each structure can be extracted and averaged. This is called subtomogram averaging and will give higher-resolution structures [29].

4.1 Procapsids

The capsid of a phage has a precursor formation, named the procapsid, during the assembly process (Figure 2). Scaffolding proteins (SPs) drive the assembly process by chaperoning major capsid protein (MCP) subunits to build an icosahedral procapsid that is later filled with dsDNA. The SPs are bound to the portal complex during formation of a procapsid with scaffolding inside. The sequence of conformational changes from a procapsid to the phage capsid where genome has been packed is named as the maturation process and goes through a series of intermediates [19, 38, 39, 40]. Some phages like HK97 and T5 do not have a separate SP; instead, the capsid protein is fused with a scaffolding domain at the N-terminus. As soon as the procapsid is assembled, the scaffolding domain is cleaved off and then like the separate SP will be removed from the capsid to make room for the genome [38, 39]. Structures of procapsids and mature virions have been determined for a number of phages (Table 1). The spherical capsid shell expands during maturation and becomes thinner due to alterations in the inter- and intra-subunit contacts.

4.2 Capsids

Most tailed phages have capsids of an icosahedral shape formed by multiple copies of one or more proteins. Icosahedral capsids are characterised by 12× fivefold, 20× threefold and 30× twofold axes, which give rise to 60 copies of the major independent parts [41]. A triangulation number (T number) describes the number of copies of the same protein within the independent part of the icosahedral lattice. The overall number of proteins in the virus corresponds to the T number multiplied by 60; for example, a T = 3 virus has 180 subunits [41]. Oligomers of the proteins that are located on the fivefold axes are referred to as pentons, while those complexes that are located on the faces of the icosahedron and form oligomers from six subunits are named as hexons.

HK97 phage. The first structure of a phage capsid was solved for the SiphoviridaeHK97 phage (a mutant without the PP and tail, diameter ~650 Å, T = 7) at 3.6 Å resolution [19] by X-ray crystallography. This structure revealed a new type of protein fold, which has been found in many other phage capsid proteins (CP) despite low sequence identity (Table 1). Later, the structure was improved to 3.45 Å resolution [42]. This fold is also found in distantly related icosahedral tailed viruses that infect halophilic archaea [43] and human pathogens such as Herpesviridae [44, 45, 46]. The characteristic features of the HK97-fold are an N-arm, a peripheral P-domain with a long helix and a β-sheet, an axial A-domain and a long E-loop that fills the region between adjacent threefold axes (Figure 3A). The HK97 capsid is held together by molecular chain mail [19]. The two antiparallel β-strands in the E-loop are terminated by a loop, containing Lys169. This residue forms an isopeptide bond with the P-domain residue Asn356 of an adjacent subunit. The third residue involved is the catalytic residue Glu363 from a third subunit (Figure 3A). Conformational changes between HK97 procapsids and capsids were assessed by flexible fitting of atomic models [40]. The capsid subunits are skewed around a pseudo-twofold axis in the procapsid but form more symmetric pentons and hexons in the mature virion.

λphage. The mature capsid of the Siphoviridae phage λ (diameter ~600 Å, T = 7) is stabilised with the help of a decoration protein gpD which is attached to the threefold vertices. A procapsid structure was determined with a resolution between 13.3 and 14.5 Å and a mature capsid at 6.8 Å [47]. The capsid protein gpE of the mature capsid shows clearly the HK97-fold so the HK97 model was used for rigid body fitting into the capsid [47]. However, the A-domain gave a poor fit so it was treated as a separate rigid body and was found to be rotated 15° clockwise compared with HK97. There was unassigned density, which could fit the extra 59 residues in the λ phage. The crystal structure of gpD (1.1 Å) [48] was fitted into the cryo-EM capsid map and, when combined with the HK97 model, showed how gpD is held in place at the capsid threefold axis.

ε15 phage. The structure of gp7, the MCP of the Salmonella phage ε15, was determined by cryo-EM (4.5 Å) [49] and showed a fold similar to that in HK97 (Figure 3B). Later, the same group obtained a better resolution structure (~3.5 Å) [50] and, using their previous 4.5 Å structure for gp7, computationally analysed possible different gp7 conformations within EM density obtained from averaging the individual subunits in one asymmetric unit. They found that two models could be fitted in the structure: one that was consistent with the previous interpretation [49], and the other had a strand swap of the β-strands in the P-domain before the two helices in the A-domain. The strand order was 4-3-1-5-2, but in the swapped model, it was now 5-4-2-3-1. The model with the strand swap provided a better visual fit in the refined map [50].

P22 phage. Structures of a procapsid and a heat-expanded capsid of the PodoviridaeP22 phage (diameter ~620 Å, T = 7) were determined by cryo-EM at 9.1 and 8.2 Å, respectively [58]. This heat-expanded capsid was composed only of hexons with wide openings where the pentons would be. The MCP gp5 revealed the HK97-fold, but there was an extra domain (residues 223–349) with an immunoglobulin-like telokin domain [64]. Later, the procapsid and capsid structures were determined by cryo-EM at 3.8 and 4.0 Å resolution, respectively [59]. It was also found that gp5 has the HK97-fold with extra density above the E-loop corresponding to the telokin domain (Figure 3C). A model built from a cryo-EM map of P22 (3.3 Å) [60] identified the interactions that stabilise the capsid. In the mature virion, the N-arm forms an antiparallel β-strand pair between neighbouring subunits around the threefold axis. A second set of interactions involve hydrogen bonds and salt bridges between adjacent subunits involving the A-domain, the E-loop and the I-domain [60].

φ29 phage. The podovirus φ29 is a relatively small phage (prolate icosahedra, height ~540 Å, diameter ~450 Å) that requires pRNA along with the ATPase gp16 to provide enough energy for the DNA translocation. The procapsid consists of the MCP gp8, the SP gp7, the head fibre protein gp8.5, the connector gp10 and a pRNA. After DNA packaging, the pRNA and ATPase come off the procapsid and are replaced by the gp11 and gp13 underneath the connector, gp29 at the end of the tail and the appendages (gp12*) which are attached to gp11 and gp13 [65]. During maturation an 18 kDa fragment of gp12 is cleaved off to give gp12* found in the appendages whose role is to adsorb the virion on the host cell. A fibreless, isometric φ29 variant capsid cryo-EM structure (7.9 Å) showed that gp8 has a structure with the HK97-fold but with extra density [66]. Domain profile-searching algorithms [67] showed that residues 348–429 at the C-terminus were found to be 32% identical to a BIG2 domain consensus sequence (group 2 bacterial immunoglobulin-like domains). An asymmetric reconstruction of fibreless full (7.8 Å) and empty (9.3 Å) capsids by cryo-EM revealed the interactions between the capsid shell and DNA [56]. All these interactions were in similar or identical locations in most of the gp8 subunits. The most prominent contact was at the end of a long tubular piece of density, which after fitting a HK97 homology model could be assigned to the N-terminal end of the HK97 long helix.

T4phage. The protein elements of the Myoviridae phage T4 (prolate icosahedra, height ~2000 Å, diameter ~900 Å) and its overall organisation have been extensively studied by X-ray and EM [62, 68, 69, 70]. The procapsid of T4 contains two proteins gp23 and gp24 which have 22% sequence identity. During maturation the gp21 protease cleaves off 65 N-terminal residues from the capsid protein gp23 and 10 N-terminal residues from the vertex protein gp24 to produce gp23* and gp24*, respectively. In the mature capsid, gp23* forms 120 hexons, and 11 capsid vertices are formed by gp24* proteins, while the 12th is occupied by a dodecamer of gp20 PP. T4 has two decoration proteins Soc and Hoc [62]. A crystal structure of gp24 (2.9 Å) [61] showed a domain with the HK97-fold and a 60 residue insertion I-domain located on the outer capsid surface (Figure 3D). The 3.3 Å cryo-EM reconstruction of the isometric capsid of T4 [62] allowed the structure of gp23* and gp24* to be determined. The I-domain linker, missing from the crystal structure of gp24, could be seen and interacts with a neighbouring gp24* molecule to stabilise the capsid. The structure of gp23* is similar to gp24* but with an extra compact region formed by residues 66–93, termed the “N-fist” prior to the N-arm residues 94–110 [62].

Crystal structures were obtained for the Hoc protein from the T4-like phage RB49 with the capsid-binding C-terminal domain 4 missing [71] and Soc protein from the T4-like phage RB49 [72]. The Soc molecules, which are required for capsid stability, interact with three gp23* subunits [62] although not all binding sites were fully occupied possibly due to differences in the gp23* I-domain linkers. The immunogenic outer capsid Hoc protein was found in two different sites within the asymmetric unit: at the centre of the hexon near the icosahedral threefold axis and in the hexon close to the fivefold axis [62]. The density of Hoc near the threefold axis was less interpretable than that near the fivefold axis.

HSV-1 virus. Although it is not a phage, the human herpesvirus HSV-1 capsid (1250 Å, T = 16) is a close relative and undergoes a pathway of self-assembly similar to that of dsDNA phages [73]. The virion is characterised by the following features: envelope, tegument, capsid and the viral genome. There are three types of HSV capsids: A-capsids have neither DNA nor the SP, B-capsids have the SP but no DNA and C-capsids contain DNA but no SP. The MCP VP5 forms pentons and hexons and VP26 binds to the VP5 hexons. A triplex of VP19C and VP23 found between capsomers [45]. The upper domain of residues 451–1054 was crystallised and the structure was determined at 2.9 Å. The structure of the whole virion of HSV-1 was determined at ~7 Å resolution [45]. The model of HK97 capsid protein was fitted to the lower domain of VP5 where the E-loop and N-arm were visible, the spline helix was longer and the central channel was wider. Unlike HK97, the E-loop does not form the covalent cross-links or reach an adjacent capsomer. Instead, it interacts with adjacent subunits, lower and middle domains of same VP5 subunit and a triplex molecule. A structure of HSV-1 with its capsid-associated tegument complex (CATC) has been obtained at 4.2 Å [63]. VP5 had the HK97-fold with six additional domains. The two β-barrels in HSV Tri1 (VP19c) and Tri2 (VP23) resemble the homotrimers found in proteins like gpD of phage λ.

4.3 Connectors

In phages and herpesviruses, one of the fivefold vertices of the capsid is replaced by a head-to-tail interface (HTI) [30], which is a multi-protein complex (connector). In all phages the HTI provides a platform for docking of preassembled tails in Sipho- or Myoviridae or initiates the assembly of a short tail in Podoviridae [30]. The HTI comprises a portal complex (PP) and head completion proteins (Figure 2) that serve as a valve for closing the channel and keeping the phage genome inside the capsid at high pressure and only opens to allow genome release from the capsid (under natural conditions) as soon as the phage becomes tightly attached to a host cell.

All currently known PPs are homo-dodecamers when extracted from the viral capsids, as that symmetry is imposed during self-assembly in vivo. However, naive assemblies in vitro of the PP complexes have some variations in their rotational symmetry with 13-mers being observed for SPP1, T7 and HK97 [31, 33, 74]. HSV has been shown to have 11-fold, 12-fold, 13-fold and sometimes even 14-fold symmetry [34]. While monomers of the different PPs vary in size, all of them share a common fold—shown by EM and X-ray structures that were obtained for the φ29, SPP1 and P22 portals [75, 76, 77, 78] and by cryo-EM for T7 and T4 (Table 2) [69, 79]. All known PP monomers are characterised by four domains: clip, stem, wing and crown (Figure 4) [77]. The clip domain is exposed to the capsid exterior and involved in binding to the terminase for DNA packaging [75, 80, 81] and later to a head completion protein during the HTI assembly [82]. The first high-resolution structure of a phage PP was obtained for the φ29 phage (Figure 4A, [75]). The clip domain is linked to the wing region through a stem that comprises typically two α-helices and the outer loops (Figure 4B,C). X-ray structures of PP from φ29 and SPP1 phages revealed major helical components that form the central channel through which DNA enters and exits the capsid. The structures of other PPs obtained later have confirmed that this is a conserved element characteristic for all known PPs. The wing domain radiates outwards from the central axis and has an α-helix, which is the longest one and serves as a spine of the wing. It has an α/β sub-fold at its periphery [77]. The crown domain consists of α-helices and is relatively small in SPP1 and surprisingly long (213 aa) in phage P22 (Figure 4B,D, Table 2).

SPP1 phage. The SPP1 phage connector has been studied for nearly two decades; the SPP1 PP structure was determined by X-ray crystallography, and all other portal complexes are compared with it (Figures 4B,C and 5A,B), but this structure was a 13-mer [31]. The HTI of SPP1 extracted from the capsid was a stable complex composed of the PP gp6, the adaptor protein (AP) gp15 and the stopper (SP) gp16, all organised as three stacked cyclical homo-oligomers [82, 83, 84] (Figure 5A,B). The cryo-EM structure of the SPP1 HTI before and after DNA release was obtained by cryo-EM at ~7 Å resolution, where the HTI is bound to the tail [82] with gp16 acting as a docking platform for the SPP1 preassembled tail [85, 86]. Binding of the tail induces changes in the position of the gp16 residues Ile9 to Thr33 that close the central channel of the connector.

HK97 phage. There is no structure of the PP gp3 of the HK97 phage, but structures of gp6 and gp7 that correspond to the AP gp15 and SP gp16 of SPP1, respectively, were determined by X-ray analysis [74]. The 2.1 Å crystal structure of the gp6 AP revealed that it forms a 13-mer during crystallisation. A model for a dodecameric ring of gp6 was constructed from a monomer taken from the 13-mer and fitted into a cryo-EM map of SPP1 [83]. This fitted well in size and shape, but the helices of HK97 gp6 did not fit well into the densities of the SPP1 connector EM map which suggested that the assembly into a 13-mer in the absence of other phage components may produce a different conformation [74].

P22 phage. The HTI of the P22 phage consists of two proteins, the PP gp1 and the AP gp4. The first structural organisation of the P22 HTI complex was obtained by cryo-EM at a resolution of 9.4 Å [91]. A crystal structure (3.25 Å) was obtained for the PP by using low-resolution EM data for phasing (Figure 5C,D [78]). The complete polypeptide chain was traced apart from a loop between residues 464 and 492, and loop modelling was used to build this area from a 9.2 Å cryo-EM map [88]. The overall height is ~300 Å with the gp4 AP forming a dodecameric ring below the PP. The PP of P22 has the same fold in its central channel as SPP1 [90] and φ29 [88, 89] (Figures 4D,5D). The crystal structure of the full-length PP revealed that the C-terminal domain forms a ~200 Å long, α-helical barrel. At the same time, an asymmetric reconstruction of the entire P22 virion has been determined by cryo-EM at 7.8 Å resolution [92]. The 150 Å coiled-coil barrel structure extends from the PP to near the centre of the capsid. Fitting the crystal structure of the core-gp4 complex into the 7.8 Å virion density map revealed a stretch of about 21 gp4 C-terminal residues that lie wedged between the capsid and portal [92]. Overlap between gp4 and the MCP gp5 indicates that gp4 must undergo significant conformational change during phage assembly when the tail is added. A comparison of the portal position in the procapsid and the virion shows that the portal increases its contact with the capsid shell during maturation. It was proposed that a portion of the scaffold remains in place during dsDNA packaging to allow access of the gp4 C-terminus to the bottom of the portal [92]. When gp4 binds, the SP is displaced allowing the final conformational change implied by the position gp4 C-terminal polypeptide that is wedged between the capsid and the HTI.

T7 phage. The HTI of T7 was determined at 8 Å resolution [79], and the dodecameric T7 PP was found to be structurally similar to the PPs from other phages (Figure 4E). A ~12 Å resolution structure of a recombinant HTI (gp8-gp11-gp12) complex of T7 was determined by cryo-EM [87], and pseudo-atomic models were obtained using gp1 and gp4 of P22 for fitting and analysis of the T7 gp8 (PP) and gp11 (AP), respectively [78]. The T7 gp8 model was superimposed on gp10 from φ29 [75, 76], gp1 from P22 [78] and gp6 from SPP1 [77] which confirmed the presence of two stem helices, but the fold of the clip domain varies between the different PPs [87]. Previous structures of the head completion proteins have shown them to contain four helices, and when the T7 gp11 model was superimposed on gp4 from P22 and gp6 from HK97 [74, 78], the position of these four helices was conserved, but the C-termini were flexible.

T4 phage. The structure of the T4 HTI region was determined by cryo-EM for the fully assembled capsid (~17 Å) [93]. The neck region, which connects the tail to the dodecameric PP (gp20), comprises adaptor proteins gp3, gp15, gp13, gp14 and gp wac (fibritin). It was assumed that the T4 HTI would have a similar PP organisation to other phages; therefore, the crystal structure of the φ29 PP was tentatively docked into the cryo-EM map of the T4 HTI region [75, 93]. Recently, the structure of the gp20 PP from T4 was determined by cryo-EM (3.6 Å) (Figure 4F, [69]). Interestingly, a gp20-N74 construct with the 73 N-terminal residues truncated contained 95% dodecamers and 5% 13-mers in solution [69]. The dodecameric PP was ~120 Å in height and varied in diameter from 90 Å (top) to 170 Å (middle) and to 80 Å close to the capsid, while the central channel goes from 90 to 28 Å near the middle of the channel. The connection to the capsid was by the PP wing domains, and the interactions are partially hydrophobic and partially polar [69].

φ29 phage. The asymmetric 3D reconstructions of φ29 with and without DNA obtained by cryo-EM at 7.8 and 9.3 Å, respectively, showed that the PP gp10 dodecamer has elongated densities lining the central channel and tilted at ~30° to the central axis of the virion [56]. These cylindrical densities correspond to the α-helices seen in the crystal structure of the φ29 PP [76]. The density of the clip domain in the cryo-EM map lies further away from the PP axis than in the crystal structure possibly due to a different conformation of the PP within the fully assembled phage. Two cylindrical columns of high density were observed within the virions: one in the upper part and another at the bottom of the HTI. These densities were assigned to DNA based on the diameter, intensity and their location. The φ29 DNA is visible as ringlike densities below the PP, and then DNA stretches into the tail to about ~100 Å [56]. The DNA appears to contact with the PP crown domain and then with the density corresponding to the tunnel loops located between the PP crown and stem domains. These tunnel loops in the narrowest part of the connector channel were found in the SPP1 phage PP and are believed that they play a role in DNA translocation [77, 94]. The φ29 DNA appears to be clamped at the top of the tail tube [56].

HSV-1 virus. Herpes simplex virus (HSV-1) has its DNA packaged into the capsid through a portal channel of the PP complex (pUL6) [95]. The structure of a dodecameric HSV-1 PP has been determined by cryo-EM at 16 Å resolution from purified portals [34]. The structure showed a close resemblance to the SPP1 PP [83]. The PP is about the same size as the pentons that occupy the other fivefold vertices, which explains the difficulty in localising the portal density in images of HSV capsids unlike in phages, which have a tail. The PP, pUL6, was well defined in the A-capsid structure located at one fivefold vertex on the outer surface of the capsid as shown by cryo-ET [96]. There is also a strong density within the portal channel and inside of the capsid, which is interpreted as the end of DNA as seen in φ29 and SPP1 [56, 82].

4.4 Tails

The tail organisation in phages depends on their type: Siphoviridae have long flexible tails, and Podoviridae have very short tails that mostly consist of the adhesive device, while Myoviridae have rigid long contractile tails that consist of a number of different proteins forming the inner rigid tube and the outer contractile sheath. Siphoviridae and Myoviridae have an independent pathway for assembly of their tails and are attached to the capsid after it has been packed with genome. However, in Podoviridae the tails are assembled on the capsids after DNA packaging as the last step of self-assembly (Figure 2, Table 3). The long tails of Siphoviridae are composed of tail proteins (TPs) that form circular oligomeric rings with three- or sixfold rotational symmetry. The rings are assembled around a tape measure protein (TMP) that defines the length of the tail and are stacked on the top of each other with helical symmetry. A tail terminator protein (TrP) caps the tail when it reaches the length defined by the TMP; the TrP serves as an interface with the capsid. When the phage interacts with the host receptor, the HTI opens and the TMP is pushed out by DNA as a result of the inner pressure of the capsid. Most long tails have a smooth outer surface, but some have appendages that protrude outwards from the tail surface.

T5 phage. The T5 phage has a long tail (1600 Å) with a diameter of 90 Å. A crystal structure has been obtained for the TP pb6 of T5 (2.2 Å) [97]. The protein consists of two domains: an N-terminal domain with two subdomains both of which comprise a β-sandwich flanked by an α-helix and a long loop (Figure 6A) and a C-terminal domain with an immunoglobulin-like fold [98]. The overall tail structure has threefold symmetry (Figure 6B) [99, 100]. Cryo-EM was used to determine the tail structure of T5 at ~6 Å resolution before and after DNA ejection [97] and the atomic model of pb6 used to interpret the results. No differences were found between the two structures, apart from the absence of the tape measure protein pb2 after DNA ejection [97].

λ phage. In the phage λ, the tail has sixfold symmetry and is composed of gpV (TP) and gpH (TMP) [101]. The N-terminal domain of gpV (gpV_N) is required for assembly of the functional phage, and the structure was determined by solution NMR [102]. There are seven β-strands, arranged into two antiparallel sheets which fold into a twisted β-sandwich (Figure 6C). The single α-helix is located at the side of the sandwich. The C-terminus of gpV (gpV_C) was shown by solution NMR to have an Ig-like fold [98].

SPP1 phage. The structures of the tails from the SiphoviridaeSPP1 before and after DNA ejection were determined using negative stain EM at ~14.5 Å resolution [85]. This tail is ~1600 Å long and consists of three proteins gp17 and gp17* that form the tail tube and the TMP gp18. Even at low resolution, the structures revealed movements in the positions of inner domains gp17 and gp17* after DNA ejection [85]. The ratio of proteins gp17 and gp17* within the tail complex suggests that the tail has to have threefold symmetry. Reconstructions of mutants comprising either gp17 or gp17* were obtained and demonstrated sixfold symmetry. A comparison of structures indicated that protein gp17* has an immunoglobulin domain located on the outer surface of the tail (Figure 6D,E) (Orlova, Personal communication).

T4 phage. Myoviridae have contractile tails with a sheath that surrounds a central tail tube. On infection, the tail sheath contracts allowing the tail tube to penetrate the outer membrane of the host cell. The structure of the T4 phage (a representative of Myoviridae) tail is well studied. It consists of a rigid tube, composed of multiple copies of gp19, surrounded by contractile sheath from gp18 subunits [93]. A structure of the central tube at 3.4 Å has been obtained by cryo-EM and showed sixfold symmetry [112] with an axial rise for the helical unit of ~40 Å. This resolution revealed the strands of the β-sheets indicating that four strands from one subunit become part of a continuous helical β-sheet lining the inner channel of the tail (Figure 6F). The structure of the T4 contracted tail was obtained at 17 Å resolution, and the tail sheath protein gp18 was found to be arranged into 23 hexameric rings [93]. A crystal structure of a gp18 mutant missing the C-terminal domain [114] was used as the basis for identifying domains in gp18. A homology model based on other Myoviridae tail sheath structures [115] was used to localise the C-terminal domain [113].

4.5 Adsorption apparatus

Most Siphoviridae phages have an oligomeric ring formed by distal tail proteins (DTPs), which is attached to the last ring of the tail tube [116, 117]. The DTP ring usually serves as an apparatus to recognise and connect to receptor-binding proteins; sometimes, this interaction is assisted by tail fibres found in T4, T5 and other phages. The DTP of SPP1 does not have the fibres [118]. Many phages that infect Gram-negative bacteria have lysozyme-like proteins on the ends of their tails, which enter the periplasm to digest the peptidoglycan barrier [119].

P22 phage. Podoviridae phage tails have a central needle with trimeric appendages (or spikes) around it, and the part of the tail attached to the capsid could be considered as the baseplate. The short tail of the podovirus P22 has been studied by cryo-EM of the entire virion [120, 121]. The structure of the P22 tail was obtained at 9.4 Å and aided understanding of its organisation [91]. The 2.8 MDa multisubunit complex is formed by the dodecameric PP gp1, 6 trimeric tailspikes of gp9, 12 copies of the tail accessory protein gp4, a hexon of gp10 and a trimer of the tail needle gp26 (Figure 7A). The proteins gp4 and gp10 form a HTI on which the tail assembles and are attached to the PP, while the N-terminal head-binding domain of the outer tailspikes (gp9) attaches to the interface of the gp4 and gp10 subunits. The second larger receptor-binding domain of gp9 contacts and destroys the cell surface lipopolysaccharide [121, 122]. Crystal structures have been obtained for both gp26 [123] and gp9 [108, 109], and these were fitted into the cryo-EM map to find how the different proteins hold the complex together. The tail needle gp26 is folded as triple-stranded coiled coil. The gp9 head-binding domain has a β-helical domain, and the receptor-binding domain is a triangular β-prism (Figure 7B) [91]. The asymmetric cryo-EM structure of P22 (7.8 Å) allowed a detailed analysis of the interactions between gp9 and the gp4–gp10 interface by fitting the gp9 and gp26 crystal structures and models of gp1, gp4 and gp10 [92].

SPP1 phage. The SiphoviridaeSPP1 phage has the long flexible tail. A negative stain reconstruction of the adsorption apparatus revealed a hinge connection between the tip and the tail tube, allowing bending angles as high as 50° [85]. The gp24 protein keeps the tail closed before DNA ejection by forming a cap and is located between the tail and the tip. The first protein in the tip after the cap is gp21, and a structural similarity has suggested that SPP1 gp21 has a fold like the P22 tailspike [85]. When the P22 tailspike is fitted to the SPP1 density, the main domain of the P22 tailspike [124] occupies ~70% of the broad flattened area. The most remote protein in the tip is gp19.1, and the predicted secondary structure was structurally similar to the head-binding domain of the P22 tailspike [124]; and fitting three copies of the P22 trimer accounted for all the density in that region. During infection the tip is lost so DNA can pass into the cell and the cap remains in an open state.

T5 phage. The crystal structure of the T5 DTP pb9 has shown that it has two domains. The A-domain has a barrel-like fold with structural similarity to the N-domains of other phage DTPs [118, 125, 126]. In spite of low sequence identity, these proteins form a hexameric ring that occupies the central core of the baseplate. The peripheral B-domain has an oligosaccharide-/oligonucleotide-binding (OB) fold [127]. The attachment of phage T5 to the host cell is assisted by three side tail fibres attached to the distal end of the tail [107, 127, 128], and they are homo-trimers of the pb1 (1396 aa). The trimeric structure of the receptor-binding carboxy-terminal domain 970–1263(aa) was determined at 2.3 Å using X-ray crystallography [107] and could be divided into five different regions (Figure 7C) based on the structure of the P22 spike [124]. The N-terminal region (989-1009 aa) is shaped by the β-strands of the three monomers that wrap around each other to form a threefold beta-helix [124, 129]. The first “interdigitated” region (ir1) is followed by a triangular domain (1010–1129 aa) where three concave β sheets form a β-prism (td1). The second interdigitated region ir2 (1130–1160 aa) also forms a short triple beta-helix. A second triangular domain td2 (1161–1238 aa) is a β-prism like td1. At the distal end of the fibre, the third interdigitated region (aa1239–1263), ir3, forms a tapered triple-helical structure making the end of the structure pointed (Figure 7C). There is some similarity in the structure with the P22 tailspike [124] as both have a β-helical domain, an ir region, a triangular beta-prism domain and a second ir domain (called caudal fin). The triangular β-prism of P22 is the most similar to td2 of pb1 and has the same topology.

TW1 phage. TW1 has an unusual tail organisation for a siphophage, as a cryo-EM reconstruction of the tail (23.5 Å) [55] revealed six spikes on the distal end from the head. They are attached to the central tail tube, similar to the spikes seen in podophages P22 and Sf6 [120, 130] (Figure 7D). The TW1 gp19 tailspike (TS) protein is homologous to the TS protein of the podophage HK620 [131] so the crystal structure of the HK620 TS protein was fitted into the TW1 appendages. The TW1 gp19 TSs are thought to be attached to the phage via the DTP gp15 protein. However, the size of TW1 gp15 and the EM density suggest that this protein does not have a peripheral OB-fold domain as seen in the DTP of phage T5 [127]. Below gp15 are gp16 and gp18, which form the central tip of the phage tail (Figure 7D) and are similar to phage λ proteins gpL and gpJ, respectively [132]. At the tip of the tail is gp27 (Figure 7D) which is homologous to peptidoglycan-degrading enzymes. Many phages that infect Gram-negative bacteria have lysozyme-like proteins in their tails which enter the periplasm to digest the peptidoglycan barrier [119].

φ29phage. The tail of φ29 has 12 appendages, which are similar to the tailspikes of phage P22 and are attached to the bulge of densities close to the capsid [133]. Each appendage is a trimer of gp12* (the cleavage product of gp12 which during maturation loses an 18 kDa C-terminal fragment). Although there is no sequence similarity with the P22 tailspike, the P22 tailspike domain structure gave a good fit into the peripheral component of the φ29 appendages [65, 124]. A construct of gp12 residues 89–854 was cleaved in vivo to give an N-terminal fragment (up to Ser691) and a C-terminal fragment (from Asp692) and crystal structures obtained for each [105]. They are both trimers, and the N-terminal part attaches to the virion and has three domains: D1* is a coiled coil, D2 is mostly a β-helix and D3 is also a β-helix (Figure 7E). The C-terminal domain D4 acts as a chaperone for trimer assembly and is cleaved by autocatalysis. The φ29 structure attached to the lipid bilayer has been obtained by cryo-ET (34 Å) [134]. The structure is comparable to cryo-EM structures of mature φ29 [56, 133, 135]. Tomographic reconstructions demonstrated the different stages of infection [134]. In the adsorption stage, the phage is tilted to the cell wall, and both the appendages and the tail seem to contact the cell surface. The tail tip protein helps the phage penetrate the cell wall. When it contacts the cytoplasmic membrane, a pore is created which allows the genome to be injected into the cell.

T4 phage. The structure of the baseplate in Myoviridae is complex as illustrated by the T4 phage. The sixfold symmetric baseplate is 270 Å long and about 520 Å in diameter at the base and is connected to the distal end of the tail [136, 137]. It is composed at least by 16 different proteins [137]. A star-shaped baseplate is formed by sequential binding of four different proteins to form a wedge shape [137]. Six wedges are arranged around the independently assembled hub. Finally, other proteins are added to form the complete baseplate. Once gp48 and gp54 have bound to the top of the central hub, polymerisation of the tail tube is initiated, and after gp25 has attached to them, then polymerisation of the sheath is initiated [138]. Crystal structures of these constituent proteins were fitted into EM structure, and this showed the location of the proteins [137]. Six long fibres and six short fibres are attached to the baseplate. The long fibres reversibly interact with the cell surface receptors [139]. After recognition, the baseplate comes closer to the cell surface allowing the six short tail fibres to bind irreversibly to the cell outer membrane. This process is accompanied by a large conformational change in the baseplate from a “high-energy” to a “low-energy” structure [93, 140]. This induces contraction of the tail sheath and allows the inner tail tube to pierce the outer host cell membrane and penetrate the inner membrane so that the genome is transferred directly to the host’s cytoplasm.

The structure of the T4 baseplate was assembled in vitro from gp10, gp7, gp8, gp6 and gp53, and the crystal structure was determined (4.2 Å) [141]. This indicated interesting differences compared to the structures when they are separately crystallised. However, about two-thirds of the structure was missing, but a cryo-EM structure of the same construct (3.8 Å) provided the positions of these missing parts [142]. The structures of T4 baseplate in its pre- and post-host attachment states were determined at 4.11 and 6.77 Å, respectively, by cryo-EM [111]. By combining high-resolution structures of the individual baseplate proteins, the authors were able to build a pseudo-atomic model for the baseplate proteins. The crystal structure at 2.9 Å of the gp5–gp27 cell-puncturing device was fitted into the EM structure (Figure 7F) [143]. Positions of gp27, gp5C (the C-terminal β-helix domain of gp5) and gp5* (the N-terminal OB-fold domain and the lysozyme middle domain) were identified. A monomeric protein gp5.4 caps the tip of the gp5 β-helix to sharpen the central spike [144]. During infection this spike punctures the cell membrane, and the lysozyme domain of gp5 digests the peptidoglycan in the E. coli periplasm.

ε15 phage. A 20 Å cryo-EM map of ε15 showed six gp20 tailspikes extending out from one of the fivefold capsid vertices. Each tailspike is composed of two domains [89] and has slightly different orientations with respect to the capsid. Cryo-ET has been used to show the interaction of ε15 phage with the cell and to visualise the process of how ε15 infects its host Salmonella anatum [110]. Initially, the tailspikes attach to the host cell followed by the tail hub attaching to a putative cell receptor. A bowl-shaped density was observed beneath the tail hub at the beginning of infection. It was proposed that phage indents the host outer membrane looking for a secondary receptor or for puncturing the membrane. A tunnel is established through the cell wall which allows the DNA to enter the cell.