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Automated classification of tailed bacteriophages according to their neck organization.

Lopes A, Tavares P, Petit MA, Guérois R, Zinn-Justin S - BMC Genomics (2014)

Bottom Line: Types and Clusters delineate consistent subgroups of Caudovirales, which correlate with several virion properties.Our method and webserver have the capacity to automatically classify most tailed phages, detect their structural module, assign a function to a set of their head, neck and tail genes, provide their morphologic subtype and localize these phages within a "head-neck-tail" based classification.It should enable analysis of large sets of phage genomes.

View Article: PubMed Central - PubMed

Affiliation: CEA, iBiTecS, Gif-sur-Yvette, F-91191 Paris, France. raphael.guerois@cea.fr.

ABSTRACT

Background: The genetic diversity observed among bacteriophages remains a major obstacle for the identification of homologs and the comparison of their functional modules. In the structural module, although several classes of homologous proteins contributing to the head and tail structure can be detected, proteins of the head-to-tail connection (or neck) are generally more divergent. Yet, molecular analyses of a few tailed phages belonging to different morphological classes suggested that only a limited number of structural solutions are used in order to produce a functional virion. To challenge this hypothesis and analyze proteins diversity at the virion neck, we developed a specific computational strategy to cope with sequence divergence in phage proteins. We searched for homologs of a set of proteins encoded in the structural module using a phage learning database.

Results: We show that using a combination of iterative profile-profile comparison and gene context analyses, we can identify a set of head, neck and tail proteins in most tailed bacteriophages of our database. Classification of phages based on neck protein sequences delineates 4 Types corresponding to known morphological subfamilies. Further analysis of the most abundant Type 1 yields 10 Clusters characterized by consistent sets of head, neck and tail proteins. We developed Virfam, a webserver that automatically identifies proteins of the phage head-neck-tail module and assign phages to the most closely related cluster of phages. This server was tested against 624 new phages from the NCBI database. 93% of the tailed and unclassified phages could be assigned to our head-neck-tail based categories, thus highlighting the large representativeness of the identified virion architectures. Types and Clusters delineate consistent subgroups of Caudovirales, which correlate with several virion properties.

Conclusions: Our method and webserver have the capacity to automatically classify most tailed phages, detect their structural module, assign a function to a set of their head, neck and tail genes, provide their morphologic subtype and localize these phages within a "head-neck-tail" based classification. It should enable analysis of large sets of phage genomes. In particular, it should contribute to the classification of the abundant unknown viruses found on assembled contigs of metagenomic samples.

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Assembly pathway of tailed bacteriophages. In the tailed phages, capsid assembly starts with the construction of an icosahedral protein lattice called procapsid, essentially composed of a major capsid protein (noted MCP in brown in Figure 1). At a specialized vertex of the procapsid, the dodecameric portal protein (Portal in blue) forms a channel which is the docking point for an ATPase complex called terminase. This complex normally contains multiple copies of a large subunit with ATPase and endonuclease activities (TermL in orange), and a small DNA binding subunit that recognizes the cognate viral DNA Sun et al.[20]. It translocates viral dsDNA into the procapsid cavity through the portal channel. When DNA packaging is completed, the terminase motor disassembles and the portal dodecamer recruits head-completion proteins to prevent leakage of the viral DNA. One such protein directly binds to the portal: it is called the adaptor protein (Ad in magenta); it can also be supplemented with the so-called head-closure protein (Hc in green)[18, 21–23]. Altogether the head-completion proteins provide a platform for completion of short tail assembly in Podoviridae[24, 25] as well as for docking of pre-assembled long tails in Sipho- and Myoviridae[26–28]. Located at one end of the Sipho- and Myoviridae long tails, the tail-completion protein (Tc in red) allows for the tail attachment to the head. Head- and tail-completion proteins form the head-to-tail connection and, together with the portal protein, constitute the virion’s neck. The major tail protein (MTP in kaki) is the main component of the tail tube structure. In Myoviridae, the surrounding tail sheath protein (Sheath in cyan) contracts upon host infection, initiating viral DNA injection in the host cell.
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Fig1: Assembly pathway of tailed bacteriophages. In the tailed phages, capsid assembly starts with the construction of an icosahedral protein lattice called procapsid, essentially composed of a major capsid protein (noted MCP in brown in Figure 1). At a specialized vertex of the procapsid, the dodecameric portal protein (Portal in blue) forms a channel which is the docking point for an ATPase complex called terminase. This complex normally contains multiple copies of a large subunit with ATPase and endonuclease activities (TermL in orange), and a small DNA binding subunit that recognizes the cognate viral DNA Sun et al.[20]. It translocates viral dsDNA into the procapsid cavity through the portal channel. When DNA packaging is completed, the terminase motor disassembles and the portal dodecamer recruits head-completion proteins to prevent leakage of the viral DNA. One such protein directly binds to the portal: it is called the adaptor protein (Ad in magenta); it can also be supplemented with the so-called head-closure protein (Hc in green)[18, 21–23]. Altogether the head-completion proteins provide a platform for completion of short tail assembly in Podoviridae[24, 25] as well as for docking of pre-assembled long tails in Sipho- and Myoviridae[26–28]. Located at one end of the Sipho- and Myoviridae long tails, the tail-completion protein (Tc in red) allows for the tail attachment to the head. Head- and tail-completion proteins form the head-to-tail connection and, together with the portal protein, constitute the virion’s neck. The major tail protein (MTP in kaki) is the main component of the tail tube structure. In Myoviridae, the surrounding tail sheath protein (Sheath in cyan) contracts upon host infection, initiating viral DNA injection in the host cell.

Mentions: Despite phage divergent and complex evolution, the thorough molecular analysis of a few paradigmatic tailed phages belonging to different morphological classes, such as Siphoviridae SPP1 and λ, Myoviridae T4 and Podoviridae P22 and Φ29, suggested that only a limited number of structural solutions are used in order to produce a functional virion[16–19]. To challenge this hypothesis, we searched for homologs of a set of virion proteins functionally characterized through the study of the assembly pathway of the corresponding phages (Figure1, Table 1 and Experimental procedures). Protein names sometimes differ for the various model phages that were studied, and are unified in Figure 1 for the sake of clarity. Proteins from the head (Major Capsid Protein or MCP, portal and terminase) and the tail (Major Tail Protein or MTP, sheath) of bacteriophages are generally well conserved, and could be detected with standard bioinformatics strategies. In contrast, proteins lying at the interface between the head and tail components, the so-called Ad, Hc and Tc head-to-tail connection proteins (see Figure 1 for definitions), can be much more difficult to detect due to drastic sequence divergence.Figure 1


Automated classification of tailed bacteriophages according to their neck organization.

Lopes A, Tavares P, Petit MA, Guérois R, Zinn-Justin S - BMC Genomics (2014)

Assembly pathway of tailed bacteriophages. In the tailed phages, capsid assembly starts with the construction of an icosahedral protein lattice called procapsid, essentially composed of a major capsid protein (noted MCP in brown in Figure 1). At a specialized vertex of the procapsid, the dodecameric portal protein (Portal in blue) forms a channel which is the docking point for an ATPase complex called terminase. This complex normally contains multiple copies of a large subunit with ATPase and endonuclease activities (TermL in orange), and a small DNA binding subunit that recognizes the cognate viral DNA Sun et al.[20]. It translocates viral dsDNA into the procapsid cavity through the portal channel. When DNA packaging is completed, the terminase motor disassembles and the portal dodecamer recruits head-completion proteins to prevent leakage of the viral DNA. One such protein directly binds to the portal: it is called the adaptor protein (Ad in magenta); it can also be supplemented with the so-called head-closure protein (Hc in green)[18, 21–23]. Altogether the head-completion proteins provide a platform for completion of short tail assembly in Podoviridae[24, 25] as well as for docking of pre-assembled long tails in Sipho- and Myoviridae[26–28]. Located at one end of the Sipho- and Myoviridae long tails, the tail-completion protein (Tc in red) allows for the tail attachment to the head. Head- and tail-completion proteins form the head-to-tail connection and, together with the portal protein, constitute the virion’s neck. The major tail protein (MTP in kaki) is the main component of the tail tube structure. In Myoviridae, the surrounding tail sheath protein (Sheath in cyan) contracts upon host infection, initiating viral DNA injection in the host cell.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4362835&req=5

Fig1: Assembly pathway of tailed bacteriophages. In the tailed phages, capsid assembly starts with the construction of an icosahedral protein lattice called procapsid, essentially composed of a major capsid protein (noted MCP in brown in Figure 1). At a specialized vertex of the procapsid, the dodecameric portal protein (Portal in blue) forms a channel which is the docking point for an ATPase complex called terminase. This complex normally contains multiple copies of a large subunit with ATPase and endonuclease activities (TermL in orange), and a small DNA binding subunit that recognizes the cognate viral DNA Sun et al.[20]. It translocates viral dsDNA into the procapsid cavity through the portal channel. When DNA packaging is completed, the terminase motor disassembles and the portal dodecamer recruits head-completion proteins to prevent leakage of the viral DNA. One such protein directly binds to the portal: it is called the adaptor protein (Ad in magenta); it can also be supplemented with the so-called head-closure protein (Hc in green)[18, 21–23]. Altogether the head-completion proteins provide a platform for completion of short tail assembly in Podoviridae[24, 25] as well as for docking of pre-assembled long tails in Sipho- and Myoviridae[26–28]. Located at one end of the Sipho- and Myoviridae long tails, the tail-completion protein (Tc in red) allows for the tail attachment to the head. Head- and tail-completion proteins form the head-to-tail connection and, together with the portal protein, constitute the virion’s neck. The major tail protein (MTP in kaki) is the main component of the tail tube structure. In Myoviridae, the surrounding tail sheath protein (Sheath in cyan) contracts upon host infection, initiating viral DNA injection in the host cell.
Mentions: Despite phage divergent and complex evolution, the thorough molecular analysis of a few paradigmatic tailed phages belonging to different morphological classes, such as Siphoviridae SPP1 and λ, Myoviridae T4 and Podoviridae P22 and Φ29, suggested that only a limited number of structural solutions are used in order to produce a functional virion[16–19]. To challenge this hypothesis, we searched for homologs of a set of virion proteins functionally characterized through the study of the assembly pathway of the corresponding phages (Figure1, Table 1 and Experimental procedures). Protein names sometimes differ for the various model phages that were studied, and are unified in Figure 1 for the sake of clarity. Proteins from the head (Major Capsid Protein or MCP, portal and terminase) and the tail (Major Tail Protein or MTP, sheath) of bacteriophages are generally well conserved, and could be detected with standard bioinformatics strategies. In contrast, proteins lying at the interface between the head and tail components, the so-called Ad, Hc and Tc head-to-tail connection proteins (see Figure 1 for definitions), can be much more difficult to detect due to drastic sequence divergence.Figure 1

Bottom Line: Types and Clusters delineate consistent subgroups of Caudovirales, which correlate with several virion properties.Our method and webserver have the capacity to automatically classify most tailed phages, detect their structural module, assign a function to a set of their head, neck and tail genes, provide their morphologic subtype and localize these phages within a "head-neck-tail" based classification.It should enable analysis of large sets of phage genomes.

View Article: PubMed Central - PubMed

Affiliation: CEA, iBiTecS, Gif-sur-Yvette, F-91191 Paris, France. raphael.guerois@cea.fr.

ABSTRACT

Background: The genetic diversity observed among bacteriophages remains a major obstacle for the identification of homologs and the comparison of their functional modules. In the structural module, although several classes of homologous proteins contributing to the head and tail structure can be detected, proteins of the head-to-tail connection (or neck) are generally more divergent. Yet, molecular analyses of a few tailed phages belonging to different morphological classes suggested that only a limited number of structural solutions are used in order to produce a functional virion. To challenge this hypothesis and analyze proteins diversity at the virion neck, we developed a specific computational strategy to cope with sequence divergence in phage proteins. We searched for homologs of a set of proteins encoded in the structural module using a phage learning database.

Results: We show that using a combination of iterative profile-profile comparison and gene context analyses, we can identify a set of head, neck and tail proteins in most tailed bacteriophages of our database. Classification of phages based on neck protein sequences delineates 4 Types corresponding to known morphological subfamilies. Further analysis of the most abundant Type 1 yields 10 Clusters characterized by consistent sets of head, neck and tail proteins. We developed Virfam, a webserver that automatically identifies proteins of the phage head-neck-tail module and assign phages to the most closely related cluster of phages. This server was tested against 624 new phages from the NCBI database. 93% of the tailed and unclassified phages could be assigned to our head-neck-tail based categories, thus highlighting the large representativeness of the identified virion architectures. Types and Clusters delineate consistent subgroups of Caudovirales, which correlate with several virion properties.

Conclusions: Our method and webserver have the capacity to automatically classify most tailed phages, detect their structural module, assign a function to a set of their head, neck and tail genes, provide their morphologic subtype and localize these phages within a "head-neck-tail" based classification. It should enable analysis of large sets of phage genomes. In particular, it should contribute to the classification of the abundant unknown viruses found on assembled contigs of metagenomic samples.

Show MeSH
Related in: MedlinePlus