Gene transfer agents: phage-like elements of genetic exchange

Abstract

Horizontal gene transfer is important in the evolution of bacterial and archaeal genomes. An interesting genetic exchange process is carried out by diverse phage-like gene transfer agents (GTAs) that are found in a wide range of prokaryotes. Although GTAs resemble phages, they lack the hallmark capabilities that define typical phages, and they package random pieces of the producing cell's genome. In this Review, we discuss the defining characteristics of the GTAs that have been identified to date, along with potential functions for these agents and the possible evolutionary forces that act on the genes involved in their production.

Figure 1. Comparison of gene transfer agent and transducing phage production

a | The genes encoding the gene transfer agent (GTA) particles are located on the host chromosome, and their expression leads to the production of GTA particles (black). GTA genes have never been found to excise from the genome as part of GTA production. Random DNA segments from the producing cell are packaged in the particles (blue particle heads), and only the occasional particle contains GTA genes (red particle head). For all genetically characterized GTAs, the amount of DNA packaged is insufficient to encode the phage-like structure (as indicated by the small heads). It is presumed that GTAs require lysis (dashed line) for release from cells. b | In the production of transducing phages, phage or prophage genes within the host genome are expressed, resulting in the production of phage particles (black) and replication of the phage genome (not shown). Packaging of the complete phage genome then occurs (orange phage heads), with occasional packaging of non-phage DNA (blue phage head). Note that this is an over simplification and some transducing phage particles can contain both phage and cellular genomic DNA. Tailed phage structures require lysis to be released from cells.

Figure 2. Electron micrographs of gene transfer agent particles

The estimated sizes of the particles are given in TABLE 1. a | Rhodobacter capsulatus gene transfer agents (RcGTAs). b | Dd1 particles from Desulfovibrio desulfuricans. c | Virus of Serpulina hyodysenteriae (VSH 1) particles in Brachyspira hyodysenteriae. d | A voltae transfer agent (VTA) particle in Methanococcus voltae. Parts a,c and d are reproduced, with permission, from (respectively) REF. © (1979) Elsevier; REF. © (1997) American Society for Microbiology; and REF. © (1999) Society for General Microbiology. Part b is modified, with permission, from REF. © (1987) US National Academy of Sciences.

Figure 3. Gene transfer agent-encoding gene clusters

The general organizations of genes encoding the two characterized gene transfer agents (GTAs). Encoded protein functions are indicated above, according to the literature^,, and our own analyses (A.S.L., unpublished observations), and ORF locus tags are indicated below. GTA encoding regions are in blue, and non-GTA-encoding regions are in green. Genes that have not yet been verified as having a role in GTA production are shown in white. Arrows indicate the direction of transcription. a | The Rhodobacter capsulatus GTA (RcGTA) gene cluster in R. capsulatus. The archetypal RcGTA ORFs are labelled 1–15 (REF. 37). b | The virus of Serpulina hyodysenteriae (VSH 1) gene cluster in Brachyspira hyodysenteriae. McpB, methyl-accepting chemotaxis protein.

Figure 4. Distribution of gene transfer agent genes in alphaproteobacteria and spirochaetes

a | The presence of gene transfer agent (GTA) genes within the alphaproteo-bacterial orders is shown. The number of genomes with a complete set of the archetypal 15 genes (orange), with at least one homologue of any of these 15 genes (blue) or lacking any detectable homologues (white) is indicated. We cannot exclude the possibility that, in genomes with only a few GTA gene homologues, the genes represent true prophages and not GTA genes. However, in several closely examined genomes, the evidence is in favour of true GTA gene homologues^,. The BLASTP (protein basic local alignment search tool) similarity searches were carried out on 146 alphaproteobacterial genomes listed as complete in the GenBank database in October 2011, using Rhodobacter capsulatus GTA (RcGTA) ORFs 1–15 (see FIG. 3) as queries and retaining matches with E values of <10⁻⁴. The phylogenetic relationships between orders are based on previous analysis of alphaproteobacteria. b | The distribution of virus of Serpulina hyodysenteriae (VSH 1) genes within the order Spirochaetales is represented on a phylogenetic tree. VSH 1 is produced by Brachyspira hyodysenteriae (orange). Homologues of the genes encoding VSH 1 are found only within other members of the Brachyspira genus (blue), but the organization of these genes is not syntenic to that in B. hyodysenteriae. White indicates genera in the order that do not contain known VSH 1 gene homologues. This simplified tree is based on a 16S ribosomal RNA gene phylogeny of strains with completed genome sequences, rooted with sequences from alpha-proteobacteria. The number of complete genome sequences within each genus available for analysis is indicated.

Figure 5. Evidence of purifying selection in selected gene transfer agent genes in the Rhodobacterales order of the class Alphaproteobacteria

The ratio of non synonymous to synonymous (dN/dS, or ω) codon substitution rates can be used as an indication of the selective pressure acting on a protein-coding gene. If a gene (or gene segment) is under purifying selection, non-synonymous mutations (that is, mutations resulting in a change of the encoded amino acid) will be selected against, resulting in ω < 1. In neutrally evolving proteins, synonymous and non-synonymous mutations will be fixed at approximately the same rate, resulting in ω = 1. Because different regions of a protein-coding gene may be under different selective constraints, codons can be divided into two categories: those with ω < 1 (yellow; the estimated ω is indicated on the bar) and those with ω fixed to 1 (green); the estimated proportion of codons in each category is given on the horizontal axis. Using this model (known as the M1a model), we estimated ω values for 15 GTA genes in members of the order Rhodobacterales (on the basis of alignments of homologues in 48 completed and draft genomes). The majority of the codons in all GTA genes are under purifying selection (only some genes are shown; ORF numbers are as given in FIG. 3). The M1a model fits significantly better than either a model with ω fixed to 1 across all codons or a model (M0) in which all codons have the same ω value (data not shown). Predictions for the housekeeping genes rpoB (encoding DNA-dependent RNA polymerase subunit-β) and recA (encoding DNA recombinase A), which are expected to be under strong purifying selection, are shown for comparison.