Reconstructing the molecular and biochemical make up of ancient lineages has remained a technical and conceptual challenge. This in part owes to the fact that the “gold standard” approaches towards resolving deep phylogeny such as comparative genomics and gene phylogenies do not work well for the most ancient molecules and are limited in their ability to recover deep historical events. Fortunately, we are on the cusp of a structural revolution – structural data are starting to increase exponentially, as genome data did in the last decade. With ~100,000 structures available in Protein Data Bank, and using state-of-the-art bioinformatics approaches, we can now dissect the very early evolutionary history by looking at deeper structural relationships that are often invisible to sequence-based comparisons, and specifically determine how structure and function have coevolved. Here, I discuss the application of structural phylogenomics in uncovering the history of viral proteomes. A systematic analysis of the conservation and utilization of protein fold structures in modern cells and viruses traces the path from earliest protein folds to the development of the complex protein machinery used in modern cells. The exercise also identifies unique viral protein folds that could become hot potential targets for drug industry.
Arshan Nasir completed his PhD from University of Illinois at Urbana-Champaign, USA (May 2015) under the supervision of Professor Dr. Gustavo Caetano-Anolles. He is currently serving as Assistant Professor in the Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan. He has published more than 15 papers in reputed journals such as Science Advances, Trends in Microbiology, Annals of the New York Academy of Science, Nucleic Acids Research, PLoS Computational Biology, BMC Evolutionary Biology, and others. Specifically, his work on origin and evolution of viruses has received broad attention in both electronic and social media worldwide (see http://news.discovery.com/animals/viruses-are-alive-and-are-oldest-living-creatures-150925.htm for Discovery News coverage). He is also serving as special Guest Editor for Archaea and has taken up the post of Managing Editor for Frontiers in Biosciences (starting 2017).