Major tail proteins of bacteriophages of the order Caudovirales

Abstract

Technological advances in cryo-EM in recent years have given rise to detailed atomic structures of bacteriophage tail tubes-a class of filamentous protein assemblies that could previously only be studied on the atomic scale in either their monomeric form or when packed within a crystal lattice. These hollow elongated protein structures, present in most bacteriophages of the order Caudovirales, connect the DNA-containing capsid with a receptor function at the distal end of the tail and consist of helical and polymerized major tail proteins. However, the resolution of cryo-EM data for these systems differs enormously between different tail tube types, partly inhibiting the building of high-fidelity models and barring a combination with further structural biology methods. Here, we review the structural biology efforts within this field and highlight the role of integrative structural biology approaches that have proved successful for some of these systems. Finally, we summarize the structural elements of major tail proteins and conceptualize how different amounts of tail tube flexibility confer heterogeneity within cryo-EM maps and, thus, limit high-resolution reconstructions.

Keywords: NMR; bacteriophage; cryo-EM; crystallography; phage; phage tail; protein dynamics; solid-state NMR; structural biology; virus.

Figure 1

Comparison of Siphoviridae-like and Myoviridae-like tail morphologies.A–H, Siphoviridae-like phages have a long, flexible, and noncontractile tail. I–R, Myoviridae-like phages have a long, rigid, and contractile tail with a sheath around the tail tube. The scale bar represents 100 nm. Reproduced with minor changes under a Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/) from the study by Sørensen et al. (104).

Figure 2

Typical architectures of Podoviridae-like, Siphoviridae-like, and Myoviridae-like phage virions are visualized by cross sections through T7, SPP1, and T4 phages.Myoviridae-like virions consist of a capsid (green), a head-to-tail connector (orange), and a tail tip (pink) (6). Siphoviridae-like (, 19, 24, 26, 27, 34, 105, 106) and Myoviridae-like (36, 37, 41, 44, 53) virions feature in addition a tail tube (turquoise) and in some cases—like T4 phage—a baseplate (purple) (45, 47). Furthermore, Myoviridae-like virions possess a sheath (gp18, white) assembled around the tail tube (turquoise), which contracts upon host cell recognition inducing a syringe-like piercing process (13, 59). The tail tubes are filled with tape measure proteins (gp18, gp29, white). Fiber proteins are not shown. Only noncapsid structural proteins are indicated.

Figure 3

Architecture of the tail tube of the gene transfer agent (GTA) of Rhodobacter capsulatus (76) as the most minimal MTP system.A, the MTP Rcc01691 consists of a β-sandwich–type fold (turquoise) flanked by an α-helix (pink) and the loop β2–β3. B, six MTPs form a hexameric ring by creating a 24-stranded β-barrel along β2–β3–β6.1–β5.2; herein the intermolecular interfaces are formed by β2–β5.2. C, these hexameric rings stack helically onto each other creating the hollow tail tube. Interring contacts are mostly mediated by the loop β2–β3 that folds onto the subjacent ring. D, nomenclature of subunits within two rings i and j. MTP, major tail protein.

Figure 4

Comparison of Siphoviridae-like MTPs. GTA is used as the most basic MTP system. In comparison to it, additional domains or loops are colored in pink. MTPs are labeled with system name, protein name, and Protein Data Bank ID. Ig-fold–like domains of T5 phage and λ phage are not shown. The pb6 structure was available through personal communication with the authors. GTA, gene transfer agent; MTP, major tail protein.

Figure 5

Comparison of Myoviridae-like MTPs. GTA is used as the most basic MTP system (Fig. 3). In comparison to it, additional domains or loops are colored in pink. MTPs are labeled with system name, protein name, and Protein Data Bank ID, and, in the case of T6SS, the bacterial host organism. GTA, gene transfer agent; MTP, major tail protein; T6SS, type VI secretion system.

Figure 6

The cryo-EM density of the tail tube of SPP1 phage.A, displays a local resolution distribution from 3.5 to 6 Å. High resolution at the inner surface of the tail tube allows for a straightforward positioning of the bulky amino acid side chains. However, the lack of resolution at the periphery required additional structural restraints from, in this case, solid-state NMR for a structure calculation following an integrative approach (B–F). Reproduced with minor changes under a Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/) from the study by Zinke et al. (86).