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Accueil > Départements > Virologie > Paulo TAVARES : Bactériophages des bactéries gram-positive

Publications de l’équipe


  • M. Ansaldi, L. Debarbieux, S. Gandon, M. - A. Petit, P. Tavares, et P. Boulanger, « "French Phage Network"-Third Meeting Report », Viruses, vol. 10, nᵒ 3, mars 2018.
    Résumé : In its third year of existence, the French Phage Network ( is pursuing its expansion. With more than 25 groups, mostly based in France, working on the various aspects of phage research, the network has increased its visibility, interactivity, and activity. The third meeting of the network, held on November 2017 at the Gif-sur-Yvette Centre National de la Recherche Scientifique (CNRS) campus, was a great opportunity for many young scientists to present their work and interact with more senior scientists, amongst which several were invited from abroad. Here we provide a summary of the work presented at this occasion during the oral presentations and poster sessions.
    Mots-clés : bacteria, bacteriophage, co-evolution, France, genomics, infection, PHAG+, phage therapy, resistance, structural biology, T5PHAG, VIRO, virulence.

  • L. M. Godinho, M. E. S. Fadel, C. Monniot, L. Jakutyte, I. Auzat, A. Labarde, K. Djacem, L. Oliveira, R. Carballido-Lopez, S. Ayora, et P. Tavares, « The Revisited Genome of Bacillus subtilis Bacteriophage SPP1 », Viruses-Basel, vol. 10, nᵒ 12, p. 705, déc. 2018.
    Résumé : Bacillus subtilis bacteriophage SPP1 is a lytic siphovirus first described 50 years ago. Its complete DNA sequence was reported in 1997. Here we present an updated annotation of the 44,016 bp SPP1 genome and its correlation to different steps of the viral multiplication process. Five early polycistronic transcriptional units encode phage DNA replication proteins and lysis functions together with less characterized, mostly non-essential, functions. Late transcription drives synthesis of proteins necessary for SPP1 viral particles assembly and for cell lysis, together with a short set of proteins of unknown function. The extensive genetic, biochemical and structural biology studies on the molecular mechanisms of SPP1 DNA replication and phage particle assembly rendered it a model system for tailed phages research. We propose SPP1 as the reference species for a new SPP1-like viruses genus of the Siphoviridae family.
    Mots-clés : Bacillus subtilis, Bacteriophage, BIM, complete nucleotide-sequence, crystal-structure, DBG, DNA replication, dna-replication, functional-analysis, genome organization, nucleoprotein complex, PHAG+, phage spp1, portal protein, Siphoviridae, small-subunit, spp1, structural rearrangements, to-tail interface, VIRO, virus assembly, virus DNA packaging, virus evolution.

  • P. Tavares, « The Bacteriophage Head-to-Tail Interface », Sub-Cellular Biochemistry, vol. 88, p. 305-328, 2018.
    Résumé : Many icosahedral viruses use a specialized portal vertex for genome encapsidation in the viral capsid (or head). This structure then controls release of the viral genetic information to the host cell at the beginning of infection. In tailed bacteriophages, the portal system is connected to a tail device that delivers their genome to the bacterial cytoplasm. The head-to-tail interface is a multiprotein complex that locks the viral DNA inside the phage capsid correctly positioned for egress and that controls its ejection when the viral particle interacts with the host cell receptor. Here we review the molecular mechanisms how this interface is assembled and how it carries out those two critical steps in the life cycle of tailed phages.
    Mots-clés : Bacteriophage, Capsid, DNA ejection, DNA packaging, Head-to-tail interface, PHAG+, Portal system, VIRO.


  • P. Cuniasse, P. Tavares, E. V. Orlova, et S. Zinn-Justin, « Structures of biomolecular complexes by combination of NMR and cryoEM methods », Current Opinion in Structural Biology, vol. 43, p. 104-113, 2017.

  • K. Djacem, P. Tavares, et L. Oliveira, « Bacteriophage SPP1 pac Cleavage: A Precise Cut without Sequence Specificity Requirement », Journal of Molecular Biology, janv. 2017.
    Résumé : In many tailed bacteriophages, DNA packaging is initiated by recognition and cleavage of a specific sequence pac by the small (TerS) and large (TerL) terminase subunits. It was previously shown that the SPP1 pac region has two sequences where TerS binds (pacR and pacL), flanking the segment where TerL cleaves the SPP1 DNA (pacC). However, the pac-specific sequences required to achieve this endonucleolytic cut were not established. Their characterization is essential to understand the underlying mechanism. We show that the pacR sequence localized within 35bp downstream of the pac cut can be extensively degenerated, including its c1 and c2 repeats, and that only a disruption of a 5-bp polyadenine tract impairs the pac cleavage. This result together with deletion analysis of pacL shows that the specific DNA sequences required for targeting the terminase for pac cleavage are considerably shorter than the large region bound by TerS. Furthermore, extensive degeneration of the 6-bp target sequence within pacC where pac cleavage occurs reveals that TerL maintains, remarkably, its precise position of cleavage. Studies with SPP1-related phages show the conservation of the cut position, irrespective of the sequence variation in pacC and in pacR or the changes in pacL-pacC distance. Mechanistically, our data are compatible with a model in which TerS interactions with part of the pacL sequence and a poly-A tract in pacR are sufficient to orient very accurately the TerL nuclease to a defined pacC position. They also demonstrate that the resulting precise cut at pacC is independent of the targeted DNA sequence.
    Mots-clés : Bacteriophage, DNA packaging, genome recognition, pac cleavage, PHAG+, terminase, VIRO.


  • S. Fernandes, A. Labarde, C. Baptista, L. Jakutytè, P. Tavares, et C. São-José, « A non-invasive method for studying viral DNA delivery to bacteria reveals key requirements for phage SPP1 DNA entry in Bacillus subtilis cells », Virology, vol. 495, p. 79-91, août 2016.
    Résumé : Bacteriophages use most frequently a tail apparatus to create a channel across the entire bacterial cell envelope to transfer the viral genome to the host cell cytoplasm, initiating infection. Characterization of this critical step remains a major challenge due to the difficulty to monitor DNA entry in the bacterium and its requirements. In this work we developed a new method to study phage DNA entry that has the potential to be extended to many tailed phages. Its application to study genome delivery of bacteriophage SPP1 into Bacillus subtilis disclosed a key role of the host cell membrane potential in the DNA entry process. An energized B. subtilis membrane and a millimolar concentration of calcium ions are shown to be major requirements for SPP1 DNA entry following the irreversible binding of phage particles to the receptor YueB.
    Mots-clés : B. subtilis, Bacteriophage, Calcium, Membrane potential, PHAG+, SPP1, VIRO, Virus entry, YueB.


  • Y. Chaban, R. Lurz, S. Brasilès, C. Cornilleau, M. Karreman, S. Zinn-Justin, P. Tavares, et E. V. Orlova, « Structural rearrangements in the phage head-to-tail interface during assembly and infection », Proceedings of the National Academy of Sciences, vol. 112, nᵒ 22, p. 7009-7014, juin 2015.
    Mots-clés : allosteric mechanism, B3S, Bacteriophage, Bacteriophages, Cryoelectron Microscopy, DNA gatekeeper, Genome, Viral, hybrid methods, INTGEN, Models, Molecular, PHAG+, Protein Conformation, viral infection, Viral Proteins, Viral Tail Proteins, VIRO, Virus Assembly, Virus Internalization.

  • V. Cvirkaite-Krupovic, R. Carballido-López, et P. Tavares, « Virus evolution toward limited dependence on nonessential functions of the host: the case of bacteriophage SPP1 », Journal of Virology, vol. 89, nᵒ 5, p. 2875-2883, mars 2015.
    Résumé : All viruses are obligate intracellular parasites and depend on certain host cell functions for multiplication. However, the extent of such dependence and the exact nature of the functions provided by the host cell remain poorly understood. Here, we investigated if nonessential Bacillus subtilis genes are necessary for multiplication of bacteriophage SPP1. Screening of a collection of 2,514 single-gene knockouts of nonessential B. subtilis genes yielded only a few genes necessary for efficient SPP1 propagation. Among these were genes belonging to the yuk operon, which codes for the Esat-6-like secretion system, including the SPP1 receptor protein YueB. In addition, we found that SPP1 multiplication was negatively affected by the absence of two other genes, putB and efp. The gene efp encodes elongation factor P, which enhances ribosome activity by alleviating translational stalling during the synthesis of polyproline-containing proteins. PutB is an enzyme involved in the proline degradation pathway that is required for infection in the post-exponential growth phase of B. subtilis, when the bacterium undergoes a complex genetic reprogramming. The putB knockout shortens significantly the window of opportunity for SPP1 infection during the host cell life cycle. This window is a critical parameter for competitive phage multiplication in the soil environment, where B. subtilis rarely meets conditions for exponential growth. Our results in combination with those reported for other virus-host systems suggest that bacterial viruses have evolved toward limited dependence on nonessential host functions. IMPORTANCE: A successful viral infection largely depends on the ability of the virus to hijack cellular machineries and to redirect the flow of building blocks and energy resources toward viral progeny production. However, the specific virus-host interactions underlying this fundamental transformation are poorly understood. Here, we report on the first systematic analysis of virus-host cross talk during bacteriophage infection in Gram-positive bacteria. We show that lytic bacteriophage SPP1 is remarkably independent of nonessential genes of its host, Bacillus subtilis, with only a few cellular genes being necessary for efficient phage propagation. We hypothesize that such limited dependence of the virus on its host results from a constant "evolutionary arms race" and might be much more widespread than currently thought.
    Mots-clés : Bacillus Phages, Bacillus subtilis, Gene Knockout Techniques, Genes, Bacterial, Genetic Testing, Host-Parasite Interactions, PHAG+, VIRO, Virus Internalization, Virus Replication.

  • C. Langlois, S. Ramboarina, A. Cukkemane, I. Auzat, B. Chagot, B. Gilquin, A. Ignatiou, I. Petitpas, E. Kasotakis, M. Paternostre, H. E. White, E. V. Orlova, M. Baldus, P. Tavares, et S. Zinn-Justin, « Bacteriophage SPP1 Tail Tube Protein Self-assembles into β-Structure-rich Tubes », Journal of Biological Chemistry, vol. 290, nᵒ 6, p. 3836-3849, févr. 2015.
    Mots-clés : Amino Acid Sequence, B3S, Bacteriophage, Bacteriophages, Electron Microscopy, Fourier Transform IR (FTIR), IMAPP, INTGEN, Molecular Sequence Data, PHAG+, Protein Folding, Protein Structure, Tertiary, Solid State NMR, Tail Tube, Tertiary Structure, Viral Proteins, Virion, VIRO, Virus Assembly.
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Publications majeures avant 2015

- Chaban Y., Lurz R., Brasilès S., Cornilleau C., Karreman M., Zinn-Justin S., Tavares P.*, and Orlova, E.V.* (2015). Structural rearrangements in the phage head-to-tail interface during assembly and infection. Proc. Natl. Acad. Sci. USA 112, 7009-7014.

- Cvirkaite-Krupovic V.*, Carballido-López, R., and Tavares P.* (2015). Virus evolution towards limited dependence on the non-essential functions of the host : the bacteriophage SPP1 case. J. Virol. 89, 2875-2883.

- Zairi M., Stiege, A.C., Nhiri, N., Jacquet, E.,and Tavares, P.* (2014). The collagen-like protein gp12 is a temperature dependent reversible binder of SPP1 viral capsids. J. Biol. Chem. 289, 27169-27181.

- Auzat I.*, Petitpas I., Lurz R., Weise F., and Tavares P. (2014). A touch of glue to complete bacteriophage assembly : the tail-to-head joining protein (THJP) family. Mol. Microbiol. 91, 1164-1178.

- Cornilleau C., Atmane N., Jacquet E., Smits C., Alonso J.C., Tavares P., and Oliveira, L.* (2013). The nuclease domain of the SPP1 packaging motor coordinates DNA cleavage and encapsidation. Nucleic Acids Res 41 : 340-354.

- Jakutytė L., Baptista C., São-José C., Daugelavičius, R., Carballido-López, R., and Tavares P.* (2011). Bacteriophage infection in rod-shaped Gram-Positive bacteria : evidence for a preferential polar route for phage SPP1 entry in Bacillus subtilis. J. Bacteriol. 193, 4893-4903 (journal cover).

- Oliveira, L.*, Cuervo, A., and Tavares, P. (2010). Direct interaction of the bacteriophage SPP1 packaging ATPase with the portal protein. J. Biol. Chem. 285, 7366-7373.

- Lhuillier, S., Gallopin, M., Gilquin, B., Brasilès, S., Lancelot, N., Letellier, G., Gilles, M., Dethan, G., Orlova, E.V., Couprie, J., Tavares, P.* and Zinn-Justin, S.* (2009). Structure of bacteriophage SPP1 head-to-tail connection reveals mechanism for viral DNA gating. Proc. Natl. Acad. Sci. USA 106, 8507-8512 (highlights on Proc. Natl. Acad. Sci. USA 106, 8401-8402 ; 8403-8404 and on Nature Rev. Microbiol. 7, 480-481).

- Auzat, I., Dröge, A., Weise,F., Lurz, R., and Tavares, P.* (2008). Origin and function of the two major tail proteins of bacteriophage SPP1. Mol. Microbiol. 70, 557-569. (highlight on Mol. Microbiol. 70, 549-553).

- Poh, S.L., El Khadali, F., Berrier, C., Lurz, R., Melki, R., and Tavares, P.* (2008). Oligomerization of the SPP1 scaffolding protein. J. Mol. Biol. 378, 551-564.

- Cuervo, A., Vaney, M.-C., Antson, A.A., Tavares, P.*, and Oliveira, L. (2007). Structural rearrangements between portal protein subunits are essential for viral DNA translocation. J. Biol. Chem. 282, 18907-18913.

- Plisson, C., White, H.E., Auzat, I., Zafarani, A., São-José, C., Lhuillier, S., Tavares, P., and Orlova, E.V.* (2007). Structure of bacteriophage SPP1 tail reveals trigger for DNA ejection. EMBO J. 26, 3720-3728.

- Lebedev, A.A., Krause, M.H., Isidro, A.L., Vagin, A., Orlova, E.V., Turner, J., Dodson, E.J., Tavares, P., and Antson, A.A.* (2007). Structural framework for DNA translocation via the viral portal protein. EMBO J. 26, 1984-1994.

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