Hummingbirds and phages


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As I’m sitting outside Café Vita and getting ready to work on phage subsystems, I can’t avoid being distracted by this number of bees and hummingbirds surrounding me. I have never had such a close view of a hummingbird. Because phage subsystems are keeping me still, these birds are totally peaceful around me. I am getting a really close view of hummingbirds working on sucking flowers. I have never noticed their beaks before. They are really interesting–well adapted to their feeding style (read about co-evolution of hummingbirds and their favorite flowers). And  because phage subsystems are keeping my mind busy, I can’t help but draw an analogy between phage modules and bird modules.

The hummingbird has several modules: a flight module (the unique wings),  a feeding module (i.e., the beak), a body module, etc. There may be other birds with same bodies but different beaks, same wings but different feet, and so forth. Phages are similar. Phage genomes, and subsequently their encoded proteomes, are modular: a set of clustered protein-encoding genes (Pegs) are dedicated to encode the phage heads (capsids); another set encodes the tails; a third set encodes host-specificity proteins, and so on. If a phage “decides” to “feed on” a novel bacterial host (for several reasons including the extinction of its old host), the phage will have to switch its host specificity. An entire phage can thus “exchange modules” with one that attacks the new host. For example, a phage in the human throat may face a crisis when the human host uses an antibiotic for a couple of weeks. The phage may be forced to switch hosts from streptococci (almost extinct after antibiosis) to bacteroides, for example (I’m just making this up). To do so, the phage needs proteins that are specific to Bacteroides.

Unlike birds, the phage cannot afford the slow process of mutagenesis and selection for evolving bacteroides-specific attack molecules. Instead, it would just “exchange” it with another phage that “knows how” to attack bacteroides but has been unsuccessful in replicating inside these anaerobic bacteria (probably due to bacterial immunity). The novel, re-invented, phage will keep the successful modules that replicate well (from the streptococcal phage) and the bacteroides-specific module from the less successful bacteroides phage.