The role played by viruses in the evolution of their hosts: a view based on informational protein phylogenies.

Viruses are often considered as fragments of cellular RNA or DNA that escaped a long time ago from cellular chromosomes and that evolved later on by capturing additional genes from the genomes of their hosts. However, this view has now been challenged by the discovery of surprising homology between viruses with very distantly related hosts, and by phylogenetic analyses suggesting that genes might also have flown from viruses to cells. We present here phylogenetic analyses of four proteins involved in DNA replication and synthesis of DNA precursors (DNA polymerases delta, ribonucleotide reductases, thymidylate synthases and replicative helicases) and we discuss the reciprocal roles of cells and viruses during the evolutionary history of these enzymes. These analyses revealed numerous lateral gene transfer events between cells and viruses, in both directions. We suggest that lateral gene transfers from viruses to cells and nonorthologous gene replacements of cellular genes by viral ones are an important source of "genetic novelties" in the evolution of cellular lineages. Thus, viruses have definitively to be considered as major players in the evolution of cellular genomes.

Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins.

A phylogenetic analysis of the five major families of DNA polymerase is presented. Viral and plasmid sequences are included in this compilation along with cellular enzymes. The classification by Ito and Braithwaite (Ito and Braithwaite 1991) of the A, B, C, D, and X families has been extended to accommodate the "Y family" of DNA polymerases that are related to the eukaryotic RAD30 and the bacterial UmuC gene products. After analysis, our data suggest that no DNA polymerase family was universally conserved among the three biological domains and no simple evolutionary scenario could explain that observation. Furthermore, viruses and plasmids carry a remarkably diverse set of DNA polymerase genes, suggesting that lateral gene transfer is frequent and includes non-orthologous gene displacements between cells and viruses. The relationships between viral and host genes appear very complex. We propose that the gamma DNA polymerase of the mitochondrion replication apparatus is of phage origin and that this gene replaced the one in the bacterial ancestor. Often there was no obvious relation between the viral and the host DNA polymerase, but an interesting exception concerned the family B enzymes: in which ancient gene exchange can be detected between the viruses and their hosts. Additional evidence for horizontal gene transfers between cells and viruses comes from an analysis of the small damage-inducible DNA polymerases. Taken together, these findings suggest a complex evolutionary history of the DNA replication apparatus that involved significant exchanges between viruses, plasmids, and their hosts.

Fire blight protection with avirulent mutants of Erwinia amylovora.

Fire blight is a necrotic disease caused by the bacterium Erwinia amyiovora, which affects pears, apples and ornamentals including Crataegus, Pyracantha, and Cotoneaster. The disease can be only partially controlled, through the use of resistant genotypes, cultural measures and antibacterial compounds, thus other methods must be investigated. It has long been established that avirulent isolates of the pathogen can control the disease, under experimental conditions. However, field use of avirulent isolates is not acceptable because of their unknown genetic stability. The protective ability under controlled conditions of genetically characterized avirulent insertion mutants of E. amylovora was examined. A bioassay on apple seedlings was used for the determination of the protective ability of 34 insertion mutants (hrp, dsp, ams). Some protective effect could be observed with most of the mutants tested and was dependent on the avirulent/virulent inoculum ratio as well as on the level of virulence of the pathogen; a minimal concentration of the avirulent mutant was necessary to give a significant level of protection. An early competition between avirulent and virulent strains for putative infection sites might be involved. For six of the mutants tested, the protective ability was particularly high and might be related to the alteration of regulatory functions of hrp genes. Results obtained with Ams- and Ams- Hrp- mutants suggested that the bacterial exopolysaccharide might play a role in the protection.