Data published by the International Human Genome Sequencing Consortium indicate that somewhere between 113 and 223 genes present in bacteria and in the human genome are absent in well-studied organisms—such as the yeast Saccharomyces cerevisiae, the fruit fly Drosophila melanogaster and the nematode Caenorhabditis elegans—that lie in between those two evolutionary extremes. Some researchers thought that these organisms, which arose after bacteria but before vertebrates, simply lost the genes in question at some point in their evolutionary history. Others suggested that these genes had been transferred directly to the human lineage by invading bacteria.
My colleague Victor DeFilippis of the Vaccine and Gene Therapy Institute of the Oregon Health and Science University and I suggested a third alternative: viruses may originate genes, then colonize two different lineages—for example, bacteria and vertebrates. A gene apparently bestowed on humanity by bacteria may have been given to both by a virus.
In fact, along with other researchers, Philip Bell of Macquarie University in Sydney, Australia, and I contend that the cell nucleus itself is of viral origin. The advent of the nucleus— which differentiates eukaryotes (organisms whose cells contain a true nucleus), including humans, from prokaryotes, such as bacteria—cannot be satisfactorily explained solely by the gradual adaptation of prokaryotic cells until they became eukaryotic. Rather the nucleus may have evolved from a persisting large DNA virus that made a permanent home within prokaryotes. Some support for this idea comes from sequence data showing that the gene for a DNA polymerase (a DNAcopying enzyme) in the virus called T4, which infects bacteria, is closely related to other DNA polymerase genes in both eukaryotes and the viruses that infect them. Patrick Forterre of the University of Paris-Sud has also analyzed enzymes responsible for DNA replication and has concluded that the genes for such enzymes in eukaryotes probably have a viral origin.
From single-celled organisms to human populations, viruses affect all life on earth, often determining what will survive. But viruses themselves also evolve. New viruses, such as the AIDS-causing HIV-1, may be the only biological entities that researchers can actually witness come into being, providing a real-time example of evolution in action.
Viruses matter to life. They are the constantly changing boundary between the worlds of biology and biochemistry. As we continue to unravel the genomes of more and more organisms, the contributions from this dynamic and ancient gene pool should become apparent. Nobel laureate Salvador Luria mused about the viral infl uence on evolution in 1959. “May we not feel,” he wrote, “that in the virus, in their merging with the cellular genome and reemerging from them, we observe the units and process which, in the course of evolution, have created the successful genetic patterns that underlie all living cells?” Regardless of whether or not we consider viruses to be alive, it is time to acknowledge and study them in their natural context—within the web of life.