Thinking about Gene Transfer Agent

I'm at Dartmouth for three months, working with Olga Zhaxybayeva's group to improve our evolutionary understanding of Gene Transfer Agent.  I'm writing an R-script simulation of the genetic exchange it causes (finally learning R), but my control runs with epistasis don't give the expected results.  So I'm writing this post and creating a Powerpoint deck to clarify my thinking.First, what's Gene Transfer Agent?  A number of different kinds of bacteria produce 'transducing particles' called Gene Transfer Agents.  These look line small phage capsids but they don't usually contain phage DNA; instead they contain random fragments of chromosomal DNA.  In the best-characterized GTA ('RcGTA'), these are all 4.4 kb in length, which appears to be the DNA capacity of the tiny GTA heads.  Like phage, GTA particles inject their DNA into recipient cells (usually of the same species), where it often recombines with the chromosome and can change the cell's genotype.GTA particles aren't infectious like phages are, both because they don't preferentially package the DNA that encodes them and because their heads are too small to contain this DNA.  The RcGTA head and tail proteins are encoded by a 14 kb gene cluster.  The sequences and organization of these genes strongly resemble that of homologous phage genes, so the known GTA systems are generally thought to have descended from what were integrated prophages. In lab cultures of cells with the RcGTA ...
Source: RRResearch - Category: Molecular Biology Authors: Source Type: blogs