Molecular Dissection of the Forces Responsible for Viral Capsid Assembly and Stabilization by Decoration Proteins

Abstract

Complex double-stranded DNA viruses utilize a terminase enzyme to package their genomes into a preassembled procapsid shell. DNA packaging triggers a major conformational change in the proteins assembled into the shell and most often subsequent addition of a decoration protein that is required to stabilize the structure. In bacteriophage λ, DNA packaging drives a procapsid expansion transition to afford a larger but fragile shell. The gpD decoration protein adds to the expanded shell as trimeric spikes at each of the 140 three-fold axes. The spikes provide mechanical strength to the shell such that it can withstand the tremendous internal forces generated by the packaged DNA in addition to environmental insults. Hydrophobic, electrostatic, and aromatic-proline noncovalent interactions have been proposed to mediate gpD trimer spike assembly at the expanded shell surface. Here, we directly examine each of these interactions and demonstrate that hydrophobic interactions play the dominant role. In the course of this study, we unexpectedly found that Trp308 in the λ major capsid protein (gpE) plays a critical role in shell assembly. The gpE-W308A mutation affords a soluble, natively folded protein that does not further assemble into a procapsid shell, despite the fact that it retains binding interactions with the scaffolding protein, the shell assembly chaparone protein. The data support a model in which the λ procapsid shell assembles via cooperative interaction of monomeric capsid proteins, as observed in the herpesviruses and phages such as P22. The significance of the results with respect to capsid assembly, maturation, and stability is discussed.

The phage L capsid decoration protein has a novel OB-fold and an unusual capsid binding strategy

“…Decoration proteins such as phage T5’s pb10 and T4’s hoc, have an overall Ig domain fold (Vernhes et al, 2017; Fokine et al, 2011). A second, more common type of decoration protein, exemplified by phage lambda’s gpD, P74-26’s gp87, phage 21’s SHP, and TW1 gp56, have similar polypeptide folds and form a symmetric trimer with an N-terminal β-tulip domain and an α/β subdomain that binds and stabilizes capsids through hydrophobic interfaces (Stone et al, 2018; Lambert et al, 2017). Additionally, some decoration proteins are known to bind the center of hexamers, as exemplified by protein Psu in phage P4 (Isaksen et al, 1993; Dokland et al, 1993; Banerjee et al, 2012).…”

The phage L capsid decoration protein has a novel OB-fold and an unusual capsid binding strategy

“…Decoration proteins such as phage T5’s pb10 and T4’s hoc, have an overall Ig domain fold [63,66]. A second, more common type of decoration protein, exemplified by phage lambda’s gpD, P74-26’s gp87, phage 21’s SHP, and TW1 gp56, have similar polypeptide folds and form a symmetric trimer with an N-terminal β-tulip domain and an α/β subdomain that binds and stabilizes capsids through hydrophobic interfaces [70,76]. Our work shows that Dec represents a third type of decoration protein fold (Figure 6), the OB-fold, as well as a different capsid-binding mechanism that discriminates against quasi three-fold capsid binding sites between pentamers and hexamers as well as that at the icosahedral three-fold sites.…”

Bacteriophage lambda: The path from biology to theranostic agent

“…In contrast, the protein cooperatively assembles as trimeric spikes at each of the 140 threefold axes of the expanded shell lattice (420 copies total, Figures and ), a reaction that can be performed in vitro under defined conditions (Lambert et al, ; Medina et al, ; Yang et al, ). Structural studies reveal that the base of the gpD trimer is highly hydrophobic (Yang et al, ), and our current model is that the hydrophobic patches exposed during procapsid expansion reside at the threefold axes of the shell, providing a nucleation site for spike assembly (see Box ) (Lambert et al, ; Medina, Andrews, Nakatani, & Catalano, ). Capsid decoration is essentially irreversible and is required to stabilize the shell, both from the internal stress of the packaged DNA and from environmental insult (Hernando‐Pérez et al, ; Q. Yang et al, ).…”

“…Yang et al, 2008). Importantly, the expanded, decorated shells are functional and can be packaged with viral and exogenous DNA in vitro (Lambert et al, 2017;M. M. Medina et al, 2011).…”

“…Procapsid assembly also encapsidates 10-12 copies of the phage protease, which degrades the scaffolding protein, modifies the portal structure and is autoproteolytic. The peptide fragments exit the shell to afford the mature procapsid shell insult (Hernando-Pérez, Lambert, Nakatani-Webster, Catalano, & de Pablo, 2014;Lambert et al, 2017;Nurmemmedov, Castelnovo, Medina, Catalano, & Evilevitch, 2012;Yang, Maluf, & Catalano, 2008).…”