Yesterday I found time to sit down with my colleague who works on the 'gene transfer agent' (GTA) of Rhodobacter capsulatus. This helped me sort out a few things that are known about this entity, and a few things that aren't.
Is GTA derived from phage? Almost certainly. My colleague's lab's recent work has shown that some of the genes needed for GTA production are homologs of known phage genes. Old work from Barry Mrrs' group also showed that supernatants of GTA-producing cultures contain particles that look like tiny tailed phages. However, no GTA- control cultures were examined, and these phage-like particles could be produced from a defective prophage unrelated to GTA.
GTA particles contain chromosomal DNA fragments about 4.5kb, but nothing is known about how the DNA comes to be packaged in these particles. This information is critical to understanding how evolutionary processes act on GTA.
Old Cot-curve and restriction analyses were consistent with the fragments being derived from random positions in the chromosome, but the resolution is very poor. The issue could be nicely resolved by isolating DNA from the particles and hybridizing it to Affymetrix chips. Unfortunately my colleague says that getting sufficient GTA particles is quite difficult, as yields are both very low and not very predictable. An attempt to find out whether the ends of the fragments are blunt or staggered was unsuccessful.
From an evolutionary perspective, the most critical missing pieces of information are probably whether GTA is always (or often) accompanied by the death of the producing cell, and whether genes allowing GTA production can be transferred by GTA. That's because, if the genes are anything more than accidents of evolutionary history, they must either enhance the fitness of the cells they are in or spread into new cells faster than they kill their present cells.
If cells can produce GTA without dying, they must have a way to pass the particles out through the cell membranes without destroying them. Some filamentous phages can be secreted by living cells, but I think the tailed phages GTA is thought to resemble escape only by lysing their hosts. The amounts of GTA produced are sufficiently small that this might entail death of only a tiny fraction of the culture.
And if GTA does kill its cells on the way out, GTA could persist of evolutionary time only if it either spread between cells like an infectious agent or greatly increased the fitness of its close kin. Neither of these seem very likely, but I'll post more about this later.
I've now got some old papers to read.
Why are unfalsifiable beliefs so attractive?
1 day ago in Epiphenom