Although deoxythymidylate cannot be provided directly by ribonucleotide reductase, the gene encoding thymidylate synthase ThyA is absent from the genomes of a large number of nonsymbiotic microbes. We show that ThyX (Thy1) proteins of previously unknown function form a large and distinct class of thymidylate synthases. ThyX has a wide but sporadic phylogenetic distribution, almost exclusively limited to microbial genomes lacking thyA. ThyX and ThyA use different reductive mechanisms, because ThyX activity is dependent on reduced flavin nucleotides. Our findings reveal complexity in the evolution of thymidine in present-day DNA. Because ThyX proteins are found in many pathogenic microbes, they present a previously uncharacterized target for antimicrobial compounds.
Tailed bacteriophages are the most abundant biological entities in marine environments. However, most of these marine phages are uncharacterized because few of their hosts have been cultivated. To learn more about such phages, we designed a set of degenerate PCR primers for phage T4 g23, which encodes the major capsid protein in all of the T4-type phages, an important family of the tailed phage. These primers were used to amplify g23-related sequences from diverse marine environments (fjords and bays of British Columbia, the eastern Gulf of Mexico, and the western Arctic Ocean) revealing a remarkable level of molecular diversity, which in some cases was correlated with morphological variation of the virions. Phylogenetic analysis showed that although some of these sequences were closely related to well studied subgroups of the T4-type phage, such as the T-evens, the majority of them belong to five previously uncharacterized subgroups. These data indicate that the host range of T4-type phages is much broader than previously imagined and that the laboratory isolate T4 belongs to a phage family that is extraordinarily widespread and diverse in the biosphere.diversity ͉ T4-type phage ͉ gene 23 ͉ genomics ͉ ecology B acteriophages are the dark matter of the biosphere. Numerous, ubiquitous, and inert, they become biologically active only when they infect an appropriate host among the innumerable bacteria in the environment. Phages are the most abundant entities in the biosphere: it has been estimated that the number of phage exceeds the number of bacteria by a factor of 5:25 (1, 2). Many lines of evidence indicate that their diversity is immense (3) and that only an infinitesimal fraction of the biosphere's phages have been inventoried.Exerting enormous influence over the microbial world, phage play a critical role in the nutrient and energy cycle (2, 4, 5). Phages are also believed to be a major driving force in cellular evolution, serving as the primary vector for horizontal genetic exchange (6, 7). Recent evidence suggests that phage genes have been frequently subverted to provide cellular functions (8-10). The reverse is also true; host genes have been subverted by phages for their own purposes (11,12). Such results argue that making a distinction between host and viral gene evolution may be artificial, because both systems seem to coevolve synergistically (12, 13).More than 5,000 phages have been described, and 96% of these are tailed phages (14). Metagenomic analysis of uncultured marine viral samples indicate that sequences belonging to tailed phages dominate marine phage communities (15) and transmission electron microscopy has verified that the large majority of marine viruses are tailed (16,17). It has been estimated that there are Ͼ10 30 tailed phage in the biosphere (18). Among the tailed phages, the myoviruses, those with contractile tails, are widespread and diverse. Quantitative transmission electron microscopy studies indicate that myoviruses constitute a major component of the marine phage communities...
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