Codes and Data Supporting The Paper 'Removal of Pseudomonas Type IV Pili by a Small RNA Virus'

<p>These files support the paper '<strong>Removal of Pseudomonas Type IV Pili by a Small RNA Virus</strong>' by J. Thongchol and Z. Yu, et al.</p><ul><li><strong>Langevin_simulation.zip</strong> contains fortran source code used for Langevin simulation in the paper</li><li><strong>Mat_pilin_interaction.pdb</strong> is the atomic structure of PP7 Mat protein interacting with a single T4P pilin from RosettaDock.</li><li><strong>refSpot_v06.m</strong> is the custom MATLAB code to calculate the intensity and relative position of the fluorescent foci for RNA smFISH data.</li></ul&gt

Structural Assembly of Qβ Virion and Its Diverse Forms of Virus-like Particles

The coat proteins (CPs) of single-stranded RNA bacteriophages (ssRNA phages) directly assemble around the genomic RNA (gRNA) to form a near-icosahedral capsid with a single maturation protein (Mat) that binds the gRNA and interacts with the retractile pilus during infection of the host. Understanding the assembly of ssRNA phages is essential for their use in biotechnology, such as RNA protection and delivery. Here, we present the complete gRNA model of the ssRNA phage Qβ, revealing that the 3′ untranslated region binds to the Mat and the 4127 nucleotides fold domain-by-domain, and is connected through long-range RNA–RNA interactions, such as kissing loops. Thirty-three operator-like RNA stem-loops are located and primarily interact with the asymmetric A/B CP-dimers, suggesting a pathway for the assembly of the virions. Additionally, we have discovered various forms of the virus-like particles (VLPs), including the canonical T = 3 icosahedral, larger T = 4 icosahedral, prolate, oblate forms, and a small prolate form elongated along the 3-fold axis. These particles are all produced during a normal infection, as well as when overexpressing the CPs. When overexpressing the shorter RNA fragments encoding only the CPs, we observed an increased percentage of the smaller VLPs, which may be sufficient to encapsidate a shorter RNA