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

Abstract

37The major coat proteins of dsDNA tailed phages and herpesviruses form capsids by a 38 mechanism that includes active packaging of the dsDNA genome into a precursor procapsid, 39 followed by expansion and stabilization of the capsid. These viruses have evolved diverse 40 strategies to fortify their capsids, such as non-covalent binding of auxiliary "decoration" 41(Dec) proteins. The Dec protein from the P22-like phage L has a highly unusual binding 42 strategy that precisely distinguishes between nearly identical three-fold and quasi-three-fold 43 sites of the icosahedral capsid. Cryo-electron microscopy and three-dimensional image 44 reconstruction were employed to determine the structure of native phage L particles. NMR 45 was used to determine the structure/dynamics of Dec in solution. Lastly, the NMR structure 46 and the cryo-EM density envelope were combined to build a model of the capsid-bound Dec 47 trimer. Key regions that modulate the binding interface were verified by site-directed 48 mutagenesis. 50Viral icosahedral capsids are formed from multiple copies of a single or a few types of 52 highly structurally-conserved coat proteins that encapsidate the genome [1]. The minimum 53 number of subunits needed to build an icosahedral capsid is 60 coat proteins, and the result 54 is a T=1 icosahedral geometry. There is a direct correlation between genome size and T-55 number for dsDNA containing phages. Building a bigger capsid necessitates the use of 56 more coat protein subunits, and requires that chemically identical proteins assemble into well-studied double stranded DNA (dsDNA) containing phages, the capsids have a T=7 59 geometry (see Figure 1A). These have 11 vertices formed by coat protein pentons and an 60 additional 60 hexons to create the capsid. The 12 th vertex breaks the icosahedral symmetry 61 and is occupied by a tail that specifies host binding. Estimates predict that 10 31 viruses are 62 in Earth's biosphere [3,4], with dsDNA containing bacteriophages being the most abundant. 63These phages have an immense diversity in terms of size and complexity. The highly 64 ubiquitous HK97-like fold is the building block for virtually all dsDNA containing phages, and 65 allows for enormous versatility in icosahedral geometry, that can lead to differences in 66 biophysical properties [5]. To withstand environmental stresses and the internal pressure 67 that amasses as a result of dsDNA genome packaging, some dsDNA phages encode 68 additional "decoration" proteins that bind to the exterior of their capsids and stabilize the 69 virions. How various decoration proteins recognize and bind to specific sites on capsids with 70 different icosahedral geometries is, however, still poorly understood. 71The tight packing of the dsDNA genomes into the virions of many phages and 72 herpesviruses creates enormous internal pressure (10 -60 atm) within the capsids, resulting 73 in high-energy states that prime the particles for infection, and facilitate delivery of the 74 majority of the viral genomes into the hosts [6]...

Keeping It Together: Structures, Functions, and Applications of Viral Decoration Proteins

“…In addition to its natural substrate phage L, Dec (L) can also noncovalently bind and stabilize expanded heads or mature capsids of phage P22 in vitro and in vivo [ 13 , 47 ]. This occurs because the coat proteins of phages L and P22 are highly homologous, differing in only 4 out of 430 positions (99.6% identical) [ 13 , 57 ]. P22 is often substituted as a model for phage L, owing to its extremely well-characterized genetics and biochemistry [ 47 ].…”

“…The icosahedral frameworks of spherical and prolate capsids have a basis set of 2-, 3-, and 5-fold symmetry axes, as summarized in the schematic of Figure 1 A. In addition to these true symmetry axes, there exist quasi-three-fold sites [ 57 ]. The first type occurs between hexamers on icosahedral facets as indicated by the cyan dots in Figure 1 A.…”

“…For example, Dec (L) binds type I quasi-three-fold sites between hexons 1000 times more strongly than true three-folds [ 92 ]. Structural data from cryo-EM suggests that Dec (L) discriminates binding-site topologies by forming a larger number of contacts with the higher avidity quasi-three-fold site [ 57 ]. By contrast, trimers of YSD1_16 (YSD1) create a non-covalent chainmail-like structure that includes binding sites at both three-fold and quasi-three-fold symmetry axes [ 54 ].…”

Principles for enhancing virus capsid capacity and stability from a thermophilic virus capsid structure

“…We hypothesize that the threefold/quasi-three-fold axes represent the weak points in a T=7 lattice. In support of this hypothesis, decoration proteins of T=7 Caudoviruses are commonly found at the three-fold/quasi-threefold axes (Table S2) (Lander et al, 2008;Newcomer et al, 2018;Shen et al, 2012;Wang et al, 2017). Furthermore, these axes are stabilized by covalent cross-links in HK97 phage (Wikoff et al, 2000) and F'-loop flaps in P74-26 ( Fig.…”

“…For example, phages lambda and TW1 use a very similar Decoration Protein fold (Stone et al, 2018), but the interaction of their Decarm with other capsid proteins is much more limited (Lander et al, 2008;Wang et al, 2017). Furthermore, the unrelated decoration protein of phage L does not connect with neighboring trimers, and in fact is missing at the quasi-three-fold axes (Newcomer et al, 2018). T4 phage is decorated with the Soc protein that interacts with neighboring Soc subunits at the three-fold and quasi-threefold axes; however, Soc is present in relatively low occupancy (~50%), so the cage is incomplete .…”