Genomics of Bacterial and Archaeal Viruses
Reporter: Larry H Bernstein, MD, FCAP
https://pharmaceuticalintelligence.com/?p=10187/Genomics of Bacterial and Archaeal Viruses/
Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere
M Krupovic, D Prangishvili, RW Hendrix, and DH Bamford
Over the past few years, the viruses of prokaryotes have been transformed in the view of microbiologists from
simply being convenient experimental model systems into being a major component of the biosphere. They are
- the global champions of diversity,
- they constitute a majority of organisms on the planet,
- they have large roles in the planet’s ecosystems,
- they exert a significant—some would say dominant—force on
- the evolution of their bacterial and archaeal hosts, and
- they have been doing this for billions of years,
- possibly for as long as there have been cells.
This transformation in status or, rather, our expanded appreciation of the importance of these viruses in the biosphere is due to a few significant developments in both understanding and technology.
(i) It has become clear that the population sizes of these viruses are astoundingly large. This realization grew out of electron microscopic enumerations of tailed phage virions in costal seawater, and numerous measurements in other environments have been made since then. A current estimate based on these measurements is that
- there are 1031 individual tailed phage virions in the global biosphere—
- enough to reach for 200 million light years if laid end to end—and measurements of population turnover suggest that
- it takes roughly 1024 productive infections per second to maintain the global population.
(ii) Advances in
DNA sequencing technology have led to dramatic qualitative improvements in how we understand the
- genetic structure of viral populations,
- the mechanisms of viral evolution, and
- the diversity of viral sequences.
The majority of newly determined gene and protein sequences of these viruses has no relatives detectable in the public sequence databases, and
- analysis of metagenomic data provides strong evidence that
- there is more genetic diversity in the genes of the viruses of prokaryotes
- than in any other compartment of the biosphere.
(iii) Facilitated by these conceptual and technical advances, studies of bacterial and archaeal viruses as important components of global biology have flourished. These viruses are revealed as important players in
- carbon and energy cycling in the oceans and other natural environments and
- as major agents in the ecology and evolution of their cellular hosts.
(iv) The isolation and characterization of new viruses have accelerated. This has been especially important for the archaeal viruses, where the discovery of new viruses and of new virus types had lagged behind bacteriophage discovery. For the
bacteriophages, the isolation of newly discovered viruses has helped improve the still extremely sparse coverage of sequence diversity and the narrow phylogenetic range of hosts represented by current data.
(v) High-resolution structures determined
- for capsid proteins and other virion proteins,
- together with information about virion assembly mechanisms,
- have allowed surprising inferences about ancestral connections among genes whose DNA sequences and encoded protein sequences
- have diverged to the point that they are no longer detectably related.
English: Schematic diagram of the hexon of a virus capsid (Photo credit: Wikipedia)
English: Adsorption of virions to cells. Português do Brasil: Adsorção de vírus a células. (Photo credit: Wikipedia)
Polio virus (picornavirus) (Photo credit: Sanofi Pasteur)
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