Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements

Abstract

Bordetella bacteriophages generate diversity in a gene that specifies host tropism. This microevolutionary adaptation is produced by a genetic element that combines the basic retroelement life cycle of transcription, reverse transcription and integration with site-directed, adenine-specific mutagenesis. Central to this process is a reverse transcriptase-mediated exchange between two repeats; one serving as a donor template (TR) and the other as a recipient of variable sequence information (VR). Here we describe the genetic basis for diversity generation. The directionality of information transfer is determined by a 21-base-pair sequence present at the 3' end of VR. On the basis of patterns of marker transfer in response to variant selective pressures, we propose that a TR reverse transcript is mutagenized, integrated into VR as a single non-coding strand, and then partially converted to the parental VR sequence. This allows the diversity-generating system to minimize variability to the subset of bases under selection. Using the Bordetella phage cassette as a signature, we have identified numerous related elements in diverse bacteria. These elements constitute a new family of retroelements with the potential to confer selective advantages to their host genomes.

Hypervariable loci in the human gut virome

“…Analysis of these regions revealed that 12 resembled the diversity-generating retroelement of phage BPP-1 described above (6,8). This system is comprised of ∼100-bp repeat regions, the donor TR, the targeted VR, and an RT, which is required to mutagenize the VR at positions where the TR contains an adenine (6).…”

“…A newly discovered mechanism of targeted hypermutation, particularly pertinent here, involves the Bordetella bacteriophage BPP-1, which has been shown to vary the sequence of the gene encoding its phage tail fiber to bind divergent cell-surface receptors (3)(4)(5)(6). The phage-encoded major tropism determinant (MTD) gene, which encodes the tip of the tail fiber, is subjected to targeted hypermutation by a reverse transcriptase (RT)-dependent mechanism (7,8).…”

Bacteria are small but not stupid: cognition, natural genetic engineering and socio-bacteriology

“…Interestingly, these examples all involve external proteins where structural changes are important to avoid immune recognition, to change surface attachment properties, or to permit interactions with different cell types. It is also noteworthy that bacterial DNA restructuring and protein engineering involve two features often thought to be limited to "higher" organisms: (i) repeat DNA sequences (Shapiro, 2002c) and reverse transcription (Doulatov et al, 2004).…”

“…-flagellar phase variation in Salmonella (Zieg at el., 1977) -fimbrial phase variation in E. coli (Blomfield, 2001) -Borrelia VSG expression (Barbour et al, 2000) -R64 plasmid sex pilus structure changes (Gyohda et al, 2004) -Neisseria pilus and opacity protein changes (Saunders et al, 2000) -Bordetella reverse transcriptase (Doulatov et al, 2004) 2000). Thus, the DNA segments that move through the genome, the places they move, and the sequences they rearrange can have both flexibility and predictability.…”

Reconstructing immune phylogeny: new perspectives

“…Collectively, these data underscore a role for complex RNA processing as another mechanism of immunological diversity. Other mechanisms can also introduce high levels of sequence diversity into receptor binding sites 135,136 , for example, when accompanied by an adjacent retroelement. …”