Gene transfer agent

Methods for detecting gene transfer agents. (A) Method used by Marrs in 1974. (B) Cell-free extract method.

The first GTA system was discovered in 1974, when mixed cultures of Rhodobacter capsulatus strains produced a high frequency of cells with new combinations of genes.[5] The factor responsible was distinct from known gene-transfer mechanisms in being independent of cell contact, insensitive to deoxynuclease, and not associated with phage production. Because of its presumed function it was named gene transfer agent (GTA, now RcGTA) More recently other gene transfer agent systems have been discovered by incubating filtered (cell-free) culture medium with a genetically distinct strain.[3]

Typical prophage and GTA gene clusters.

Schematic diagram of phylogenetic relationships between known bacterial gene transfer agents.

The evolutionary forces that act on bacterial gene transfer agent and the cells that produce it.

The genes specifying GTAs are derived from bacteriophage (phage) DNA that has integrated into a host chromosome. Such prophages often acquire mutations that make them defective and unable to produce phage particles.  Many bacterial genomes contain one or more defective prophages that have undergone more-or less-extensive mutation and deletion. Gene transfer agents, like defective prophages, arise by mutation of prophages, but they retain functional genes for the head and tail components of the phage particle (structural genes) and the genes for DNA packaging. The phage genes specifying its regulation and DNA replication have typically been deleted, and expression of the cluster of structural genes is under the control of cellular regulatory systems. Additional genes that contribute to GTA production or uptake are usually present at other chromosome locations. Some of these have regulatory functions, and others contribute directly to GTA production (e.g. the phage-derived lysis genes) or uptake and recombination (e.g. production of cell-surface capsule and DNA transport proteins) These GTA-associated genes are often under coordinated regulation with the main GTA gene cluster.[6]  Phage-derived cell-lysis proteins (holin and endolysin) then weaken the cell wall and membrane, allowing the cell to burst and release the GTA particles. The number of GTA particles produced by each cell is not known.

Some GTA systems appear to be recent additions to their host genomes, but others have been maintained for many millions of years. Where studies of sequence divergence have been done (dN/dS analysis), they indicate that the genes are being maintained by natural selection for protein function (i.e. defective versions are being eliminated).[7][8]

However the nature of this selection is not clear.  Although the discoverers of GTA assumed that gene transfer was the function of the particles, the presumed benefits of gene transfer come at a substantial cost to the population.  Most of this cost arises because GTA-producing cells must lyse (burst open) to release their GTA particles, but there are also genetic costs associated with making new combinations of genes, because most new combinations will usually be less fit than the original combination.[9]    One alternative explanation is that GTA genes persist because GTAs are genetic parasites that spread infectiously to new cells. However this is ruled out because GTA particles typically are too small to contain the genes that encode them.  For example, the main RcGTA cluster (see below) is 14 kb long, but RcGTA particles can contain only 4–5 kb of DNA.   

Most bacteria have not been screened for the presence of GTAs, and many more GTA systems may await discovery.  Although DNA-based surveys for GTA-related genes have found homologs in many genomes, but interpretation is hindered by the difficulty of distinguishing genes that encode GTAs from ordinary prophage genes.[7] [8]

Typical steps in the production of bacterial gene transfer agents. (1) Transcription and translation of the GTA genes. (2) Assembly of GTA structural proteins into empty heads and unattached tails. (3) Packaging of 'headful' segments of DNA into heads and attachment of tails. (4) Lysis of the cell.

In laboratory cultures, production of GTAs is typically maximized by particular growth conditions that induce transcription of the GTA genes; most GTAs are not induced by the DNA-damaging treatments that induce many prophages.  Even under maximally inducing conditions only a small fraction of the culture produces GTAs, typically less than 1%.[10][11]

The steps in GTA production are derived from those of phage infection. The structural genes are first transcribed and translated, and the proteins assembled into empty heads and unattached tails.  The DNA packaging machinery then packs DNA into each head, cutting the DNA when the head is full, attaching a tail to the head, and then moving the newly-created DNA end on to a new empty head. Unlike prophage genes, the genes encoding GTAs are not excised from the genome and replicated for packaging in GTA particles.  The two best studied GTAs (RcGTA and BaGTA) randomly package all of the DNA in the cell, with no overrepresentation of GTA-encoding genes.[10][12] The number of GTA particles produced by each cell is not known.

Genetic transduction by bacterial gene transfer agents. (1) GTA particles encounter a suitable recipient cell. (2) Particles attach to cell and inject their DNA, and cellular proteins translocate the DNA across the inner membrane. (3) DNA is degraded if it cannot recombine with the recipient genome. (4) DNA with similar sequences to the recipient genome undergoes recombination.

Whether release of GTA particles leads to transfer of DNA to new genomes depends on several factors.   First, the particles must survive in the environment – little is known about this, although particles are reported to be quite unstable under laboratory conditions.[13] Second, particles must encounter and attach to suitable recipient cells, usually members of the same or a closely related species.  Like phages, GTAs attach to specific protein or carbohydrate structures on the recipient cell surface before injecting their DNA.  Unlike phage, the well-studied GTAs appear to inject their DNA only across the first of the two membranes surrounding the recipient cytoplasm, and they use a different system, competence-derived rather than phage-derived, to transport one strand of the double-stranded DNA across the inner membrane into the cytoplasm.[14][15]

If the cell's recombinational repair machinery finds a chromosomal sequence very similar to the incoming DNA, it replaces the former with the latter by homologous recombination, mediated by the cell's RecA protein. If the sequences are not identical this will produce a cell with a new genetic combination.  However, if the incoming DNA is not closely related to DNA sequences in the cell it will be degraded, and the cell will reuse its nucleotides for DNA replication.

• Gene transfer agent-release holin family
• Horizontal gene transfer