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Journal of Virology, September 2006, p. 9331-9335, Vol. 80, No. 18
0022-538X/06/$08.00+0 doi:10.1128/JVI.01160-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS and Universités Aix-Marseille I & II, Campus de Luminy, Case 932, 13288 Marseille Cedex 09, France,1 Groupe de Recherche en Écologie Buccale (GREB), Faculté de Médecine Dentaire,2 Félix d'Hérelle Reference Center for Bacterial Viruses,3 Département de Biochimie et de Microbiologie, Faculté des Sciences et de Génie, Université Laval, Québec City, Québec, Canada G1K 7P44
Received 5 June 2006/ Accepted 21 June 2006
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Virulent lactococcal bacteriophages (infecting Lactococcus lactis) are a significant threat to the dairy industry. Hundreds of phages infecting various L. lactis strains have been isolated worldwide (11). Most lactococcal phages disturbing fermentations belong to one of three phage groups, namely, 936, c2, and P335, of the Siphoviridae family (10, 12). Members of the 936- and P335-like phage groups recognize their host through an interaction between their RBP (7) and unknown saccharidic receptors at the host cell surface (17, 18, 21).
We previously determined the crystal structures of two RBPs, from the virulent lactococcal phage p2 (936 group) (18, 21) and the temperate phage TP901-1 (P335 group) (17). Despite amino acid sequence diversity and infecting different L. lactis strains, the RBPs of these two phages are closely related and are formed of three monomers related by a threefold noncrystallographic axis. Each monomer comprises three domains: the N terminus (named shoulders), the interlaced neck, and the head domain at the C terminus. We have suggested that this last domain harbors a putative saccharide binding site and recognizes the host receptor (5, 9, 17, 18, 21).
The complete genome of bacteriophage bIL170 is available (4), and the gene coding for its RBP was recently identified (6). The deduced RBPs from phages p2 and bIL170 exhibit an overall 52% sequence identity for 267 residues. However, the first 134 residues, which correspond to phage p2 shoulders, share 89% identity, while the remaining 133 residues (the neck and head domains in the RBP of phage p2) share only 15% identity. The diversity in these host recognition domains is in agreement with their different host ranges. The lack of structural knowledge due to the absence of sequence identity prompted us to express and crystallize the RBP head domain of phage bIL170.
bIL170 head domain production and characterization. orf20, coding for the RBP of phage bIL170, was cloned in the Gateway pDEST14 vector (25) with a C-terminal His6 tag, and the resulting vector was transformed in E. coli Rosetta-pLysS strains. The head domain was cloned between residues Asn 155 and Leu 267 (Fig. 1A) using the same procedure. With both constructs, cell growth and lysis as well as protein purification were performed as previously described (17, 23, 24). Both constructs led to expression of soluble proteins, but the full-length RBP was not stable with time, in contrast to the head domain, which was subjected to binding studies and crystallization assays.
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FIG. 1. Compared sequence and structure of the RBPs from lactococcal phages bIL170 and p2. Panel A, amino acid sequence alignment of the RBP from phages bIL170 and p2 (alignment made by MULTALIN [http://prodes.toulouse.inra.fr/multalin/multalin.html]). Red shading highlights conserved amino acids. Two red arrows indicate the cloned head domain. Panel B, view of the bIL170 RBP dimer as found in the crystal. The twofold axis is vertical. Colors vary from blue to red, from N to C terminus (rainbow coloring scheme). Panel C, ribbon stereo view of the bIL170 RBP monomer (green) superimposed on the p2 RBP monomer (red). The views were made with Pymol (http://www.pymol.org).
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TABLE 1. Kd constants for three saccharides, obtained by fluorescence quenching
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The monomer has a quasidouble Greek key fold close to those found in p2 and TP901-1 RBPs (Fig. 1). After superposition with the p2 RBP head monomer, a root-mean-square deviation (rmsd) of 2.17 Å calculated for 96 residues of 110 was measured. Applying the same procedure to the RBP head of the lactococcal phage TP901-1 yielded an rmsd of 2.10 Å calculated for 94 residues of 110. Between the RBP heads of p2 and TP901-1, an rmsd value of 0.80 Å was obtained with 96 residues of 100. A dimer was present in the crystal, however (Fig. 1), and not a trimer as for the two other RBPs.
The trimeric model. It can be postulated, however, that the bIL170 RBP head is a homotrimer on the basis of several arguments. First, the amino acid identity between the shoulder domains of the p2 and bIL170 RBPs is 89% (Fig. 1A), which ensures an identical assembly for both domains. Second, the head domain of the p2 RBP alone has been revealed to be a trimer (18). Finally, the head domain of the bIL170 RBP is functional in solution. It was therefore a surprise when the X-ray structure revealed the presence of a dimer in the crystal. The molecular surface area covered upon dimerization is quite low, however, being only 490 Å2, which represents 9.2% of the whole monomer surface. It is therefore very likely that the bIL170 RBP head is a weak dimer and is the result of a crystallization artifact. We could superimpose three monomeric bIL170 RBP head domains onto the p2 RBP trimer. The resulting trimer (Fig. 2A and B) does not exhibit steric clashes involving main chains. Examination of the surface of the trimer revealed the presence of a crevice located at the interface between two monomers (Fig. 2B and C). Such crevices between monomers have been also observed in the RBPs of lactococcal phages p2 and TP901-1.
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FIG. 2. Three-dimensional structure of the trimer model of the bIL170 RBP head. Panel A, ribbon view of the trimer assembly. Colors are blue, orange, and green for monomers A, B, and C, respectively. Panel B, view of the overall molecular surface of the head domain trimer with tyrosine 226 displayed (blue and red spheres) as well as a modeled glycerol molecule (white and red spheres). Panel C, view in sphere representation of the binding crevice. The glycerol molecule in the position observed in the RBP structure of another lactococcal phage of the 936 group (phage p2) is represented as white sticks. A glycerol molecule has been modeled in the site, close to Tyr 226 (protein surface in blue; Tyr 226 and glycerol are colored yellow and red). Panel D, representation of the modeled glycerol molecule in its binding site (protein in blue; glycerol, Tyr 226, Ser 191b, and Asp 220b are colored in atom mode: C, yellow; O, red; N, blue). The putative hydrogen bonds are displayed in green (views made with Turbo-Frodo [15]).
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FIG. 3. Comparison of the RBP atomic models from four phages. Two phage RBPs are from the 936 group, namely, p2 (18) and bIL170 (this work), while the two other phages are from the P335 group, namely, TP901-1 (17) and Tuc2009 (model). RBPs are represented on the same scale, and their three domains, N-terminal (or shoulders in p2), neck, and head, have been labeled Nt, Neck, and Head, respectively. The experimentally determined structures are represented in ribbons colored by chain, blue, pink, and yellow. The analogous modeled structures are represented in gray ribbons. Gray squares or circles represent the still-unknown structures.
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As mentioned above, the search for sequences similar to the bIL170 head domain returned five lactococcal phage RBPs, those of phage bIL66 (97% identity; E = 1e56), phage P008 (95% identity; E = 1e55), phage P113G/p272 (94% identity; E = 2e54), phage bIL309 (48% identity; E = 2e22), and phage bIL286 (47% identity; E = 1e21). The first three phages are virulent and belong to the 936 group (as bIL170). Their polypeptidic chains upstream of the head domains are all 159 residues long. Due to the very high sequence identity, this chain (containing the shoulders and neck domains) should share a fold (ß-barrel) nearly identical to those of phages bIL170 and p2. In contrast, the two latter phages, which are L. lactis prophages and belong to the P335 group (as TP901-1), present a strikingly different picture. The polypeptidic chains upstream of the RBP head domains of prophages bIL309 and bIL286 are 1,333 and 703 residues long, respectively. Furthermore, while in the three former RBP shoulders the folds are formed of ß-strands, in the two latter RBPs several G-X-X-G repeat motifs are observed, a hallmark of parallel triple helical structures. A similar kind of triple-helix bundle has been observed at the N terminus of phage TP901-1, also a P335 temperate phage, but with a smaller size (30 residues) (17). Recently, the gene coding for the RBP of phage TP901-1 was successfully exchanged with the analogous gene of the temperate phage Tuc2009 (P335 group). The chimerical TP901-1 phage infected the Tuc2009 host strain efficiently and thus displayed an altered host range compared to that of the wild-type phage TP901-1 (22). Molecular biology data indicated that the temperate phage Tuc2009 has an RBP N terminus similar to that found in TP901-1 (22).
To date, with the small number of structures solved and the structural elements inferred from analysis of sequence in a structural context, it seems that virulent phages of the 936 group possess shoulders formed of an assembly of three ß-barrels, while phages from the P335 group possess a triple-helical N terminus (Fig. 3). These N-terminal domains, however, display a large variability in size, ranging between
60 and
1,300 residues. This difference in the length of the RBP domain anchoring the molecule to the phage baseplate should have a profound influence on the overall structure located at the distal part of the tail.
Our results demonstrate that the fold repertoire of RBP heads is smaller than what is suggested by sequence comparisons. With no exception to date, this fold is shared between RBPs of lactoccocal phages and their functional homologues in reo- and adenoviruses. Interestingly, functional behavior, as depicted by sugar binding, can be closely related between RBP heads displaying no sequence diversity.
Protein structure accession number. Coordinates and structure factors have been deposited with the Protein Data Bank as entry 2FSD.
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