Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements.
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.
Doulatov
Sergei
S
Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA.
Hodes
Asher
A
Dai
Lixin
L
Mandhana
Neeraj
N
Liu
Minghsun
M
Deora
Rajendar
R
Simons
Robert W
RW
Zimmerly
Steven
S
Miller
Jeff F
JF
D000222:Adaptation, Physiological / Q000235:genetics*; D001435:Bacteriophages / Q000201:enzymology / Q000235:genetics* / Q000502:physiology*; D001483:Base Sequence; D005075:Biological Evolution; D001884:Bordetella / Q000145:classification / Q000821:virology*; D019295:Computational Biology; D005814:Genes, Viral / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics*; D016679:Genome, Viral; D006790:Host-Parasite Interactions; D016296:Mutagenesis / Q000235:genetics*; D010802:Phylogeny; D011110:Polymorphism, Genetic / Q000235:genetics; D012194:RNA-Directed DNA Polymerase / Q000378:metabolism; D018626:Retroelements / Q000235:genetics / Q000502:physiology*; D012641:Selection, Genetic; D013045:Species Specificity; D014158:Transcription, Genetic / Q000235:genetics
D018626:Retroelements; D012194:RNA-Directed DNA Polymerase