Structures of Three Actinobacteriophage Capsids: Roles of Symmetry and Accessory Proteins

JM, Podgorski; Calabrese, Joshua; Alexandrescu, L.; Jacobs-Sera, Deborah; Pope, Welkin H.; Hatfull, Graham F.; White, Simon

doi:10.3390/v12030294

Cited by 17 publications

(20 citation statements)

References 58 publications

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“…Among the gut metagenome-assembled tailed phages, the putative phages OGQL01007720.1 (4.5 kbp) and OMEC01003054.1 (5.4 kbp) were predicted to adopt T = 4/3 ≈ 1.33 icosahedral capsids. The trihexagonal lattice associated with T = 4/3 ≈ 1.33 has been observed among higher T-numbers for tailed phages [19,20]. However, no major capsid protein or portal protein was annotated in those Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 2 November 2020 doi:10.20944/preprints202011.0024.v1…”

Section: Discussionmentioning

confidence: 99%

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The Missing Tailed Phages: Prediction of Small Capsid Candidates

Luque

Benler

Lee

et al. 2020

Preprint

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Tailed phages are the most abundant and diverse group of viruses on the planet. Yet, the smallest tailed phages display relatively complex capsids and large genomes compared to other viruses. The lack of tailed phages forming the common icosahedral capsid architectures T = 1 and T = 3 is puzzling. Here, we extracted geometrical features from high-resolution tailed phage capsid reconstructions and built a statistical model based on physical principles to predict the capsid diameter and genome length of the missing small tailed phage capsids. We applied the model to 3,348 isolated tailed phage genomes and 1,496 gut metagenome-assembled tailed phage genomes. Four isolated tailed phages were predicted to form T = 3 icosahedral capsids, and twenty-one metagenome-assembled tailed phages were predicted to form T < 3 capsids. The smallest capsid predicted was a T = 4/3 ≈ 1.33 architecture. No tailed phages were predicted to form the smallest icosahedral architecture, T = 1. We discuss the feasibility of the missing T = 1 tailed phage capsids and the implications of isolating and characterizing small tailed phages for viral evolution and phage therapy.

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Section: Discussionmentioning

confidence: 99%

“…The fifth element of the series is T = 3 and contains 180 major capsid proteins. Tailed phages have been observed to form capsids adopting the hexagonal and trihexagonal lattices [19,20]. But no tailed phages have been observed to form T ≤ 3…”

Section: Introductionmentioning

confidence: 99%

The Missing Tailed Phages: Prediction of Small Capsid Candidates

Luque

Benler

Lee

et al. 2020

Preprint

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“…The capsid structures of three actinobacteriophages, discovered through a collaboration with the SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) program, were recently resolved to approximately 6 Å by cryo-EM. Of these phages, two had novel decoration proteins with no known sequence homologs [ 32 ]. Similarly, 7 of 16 newly discovered Shigella -infecting phages had a novel decoration protein [ 33 ].…”

Section: Introductionmentioning

confidence: 99%

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

Dedeo

Teschke

Alexandrescu

2020

Viruses

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Decoration proteins are viral accessory gene products that adorn the surfaces of some phages and viral capsids, particularly tailed dsDNA phages. These proteins often play a “cementing” role, reinforcing capsids against accumulating internal pressure due to genome packaging, or environmental insults such as extremes of temperature or pH. Many decoration proteins serve alternative functions, including target cell recognition, participation in viral assembly, capsid size determination, or modulation of host gene expression. Examples that currently have structures characterized to high-resolution fall into five main folding motifs: β-tulip, β-tadpole, OB-fold, Ig-like, and a rare knotted α-helical fold. Most of these folding motifs have structure homologs in virus and target cell proteins, suggesting horizontal gene transfer was important in their evolution. Oligomerization states of decoration proteins range from monomers to trimers, with the latter most typical. Decoration proteins bind to a variety of loci on capsids that include icosahedral 2-, 3-, and 5-fold symmetry axes, as well as pseudo-symmetry sites. These binding sites often correspond to “weak points” on the capsid lattice. Because of their unique abilities to bind virus surfaces noncovalently, decoration proteins are increasingly exploited for technology, with uses including phage display, viral functionalization, vaccination, and improved nanoparticle design for imaging and drug delivery. These applications will undoubtedly benefit from further advances in our understanding of these versatile augmenters of viral functions.

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“…Capsid proteins in tailed phages are organized following hexagonal and trihexagonal icosahedral lattices, Fig. 1 [122] , [99] , [82] , and the double-stranded DNA genome is packed in the capsid at quasicrystalline densities [36] , [78] , [82] . The number of capsid proteins is determined by the triangulation number or T-number, which is a discrete index determining the possible capsid surfaces compatible with icosahedral symmetry [24] , [122] .…”

Section: Introductionmentioning

confidence: 99%

“…T hex and T tri are the T-numbers associated, respectively, with the hexagonal and trihexagonal lattices defined by the generalized icosahedral capsid theory [122] . The top and bottom capsid examples correspond, respectively, to phage HK97 (PDB 2 fs3; [47] and phage patience (EMDB-21123; [99] . The capsids were rendered with ChimeraX [96] .…”

Section: Introductionmentioning

confidence: 99%