Next Article in Journal
Physiological Response of Corynebacterium glutamicum to Indole
Previous Article in Journal
Burkholderia gladioli CGB10: A Novel Strain Biocontrolling the Sugarcane Smut Disease
Previous Article in Special Issue
Prophages and Past Prophage-Host Interactions Revealed by CRISPR Spacer Content in a Fish Pathogen
Article

The Missing Tailed Phages: Prediction of Small Capsid Candidates

1
Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
2
Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA
3
Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92182, USA
4
National Center for Biotechnology Information (NCBI), Bethesda, MD 20894, USA
5
Department of Physics, San Diego State University, San Diego, CA 92182, USA
6
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
*
Author to whom correspondence should be addressed.
Microorganisms 2020, 8(12), 1944; https://doi.org/10.3390/microorganisms8121944
Received: 29 October 2020 / Revised: 4 December 2020 / Accepted: 5 December 2020 / Published: 8 December 2020
(This article belongs to the Special Issue Understanding Phage Particles)
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 3348 isolated tailed phage genomes and 1496 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. View Full-Text
Keywords: bacteriophage; tailed phages; icosahedral capsids; capsid modeling; statistical learning; isolated genomes; metagenome-assembled genomes bacteriophage; tailed phages; icosahedral capsids; capsid modeling; statistical learning; isolated genomes; metagenome-assembled genomes
Show Figures

Figure 1

MDPI and ACS Style

Luque, A.; Benler, S.; Lee, D.Y.; Brown, C.; White, S. The Missing Tailed Phages: Prediction of Small Capsid Candidates. Microorganisms 2020, 8, 1944. https://doi.org/10.3390/microorganisms8121944

AMA Style

Luque A, Benler S, Lee DY, Brown C, White S. The Missing Tailed Phages: Prediction of Small Capsid Candidates. Microorganisms. 2020; 8(12):1944. https://doi.org/10.3390/microorganisms8121944

Chicago/Turabian Style

Luque, Antoni, Sean Benler, Diana Y. Lee, Colin Brown, and Simon White. 2020. "The Missing Tailed Phages: Prediction of Small Capsid Candidates" Microorganisms 8, no. 12: 1944. https://doi.org/10.3390/microorganisms8121944

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop