KOPRI Repository

Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells

Cited 4 time in scopus
Metadata Downloads
Title
Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells
Other Titles
단백체의 크기의 계통학적 추적은 단백질 구조 도메인의 점진적 누적과 초기 원시세포로 부터의 바이러스 진화를 지지함
Authors
Arshan Nasir
Gustavo Caetano-Anolles
Kim, Kyung Mo
Subject
Microbiology
Issue Date
2017
Citation
Arshan Nasir, Gustavo Caetano-Anolles, Kim, Kyung Mo. 2017. "Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells". FRONTIERS IN MICROBIOLOGY, 8(0): 1178-1178.
Abstract
Untangling the origin and evolution of viruses remains a challenging proposition. We recently studied the global distribution of protein domain structures in thousands of completely sequenced viral and cellular proteomes with comparative genomics, phylogenomics, and multidimensional scaling methods. A tree of life describing the evolution of proteomes revealed viruses emerging from the base of the tree as a fourth supergroup of life. A tree of domains indicated an early origin of modern viral lineages from ancient cells that co-existed with the cellular ancestors. However, it was recently argued that the rooting of our trees and the basal placement of viruses was artifactually induced by small genome (proteome) size. Here we show that these claims arise from misunderstanding and misinterpretations of cladistic methodology. Trees are reconstructed unrooted, and thus, their topologies cannot be distorted a posteriori by the rooting methodology. Tracing proteome size in trees and multidimensional views of evolutionary relationships as well as tests of leaf stability and exclusion/inclusion of taxa demonstrated that the smallest proteomes were neither attracted toward the root nor caused any topological distortions of the trees. Simulations confirmed that taxa clustering patterns were independent of proteome size and were determined by the presence of known evolutionary relatives in data matrices, highlighting the need for broader taxon sampling in phylogeny reconstruction. Instead, phylogenetic tracings of proteome size revealed a slowdown in innovation of the structural domain vocabulary and four regimes of allometric scaling that reflected a Heaps law. These regimes explained increasing economies of scale in the evolutionary growth and accretion of kernel proteome repertoires of viruses and cellular organisms that resemble growth of human languages with limited vocabulary sizes. Results reconcile dynamic and static views of domain frequency distributions that are consistent with the axiom of spatiotemporal continuity that is tenet of evolutionary thinking.
URI
http://repository.kopri.re.kr/handle/201206/6511
DOI
http://dx.doi.org/10.3389/fmicb.2017.01178
Files in This Item
General Conditions
      ROMEO Green
    Can archive pre-print and post-print or publisher's version/PDF
      ROMEO Blue
    Can archive post-print (ie final draft post-refereeing) or publisher's version/PDF
      ROMEO Yellow
    Can archive pre-print (ie pre-refereeing)
      ROMEO White
    Archiving not formally supported

    qrcode

    Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

    Browse