Rapid host adaptation by extensive recombination.
Experimental investigations into virus recombination can provide valuable insights into the biochemical mechanisms and the evolutionary value of this fundamental biological process. Here, we describe an experimental scheme for studying recombination that should be applicable to any recombinogenic viruses amenable to the production of synthetic infectious genomes. Our approach is based on differences in fitness that generally exist between synthetic chimaeric genomes and the wild-type viruses from which they are constructed. In mixed infections of defective reciprocal chimaeras, selection strongly favours recombinant progeny genomes that recover a portion of wild-type fitness. Characterizing these evolved progeny viruses can highlight both important genetic fitness determinants and the contribution that recombination makes to the evolution of their natural relatives. Moreover, these experiments supply precise information about the frequency and distribution of recombination breakpoints, which can shed light on the mechanistic processes underlying recombination. We demonstrate the value of this approach using the small single-stranded DNA geminivirus, maize streak virus (MSV). Our results show that adaptive recombination in this virus is extremely efficient and can yield complex progeny genomes comprising up to 18 recombination breakpoints. The patterns of recombination that we observe strongly imply that the mechanistic processes underlying rolling circle replication are the prime determinants of recombination breakpoint distributions found in MSV genomes sampled from nature.
van der Walt
Eric
E
Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa.
Rybicki
Edward P
EP
Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.|Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa.
Varsani
Arvind
A
Electron Microscope Unit, University of Cape Town, Cape Town, South Africa.|Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa.
Polston
J E
JE
Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
Billharz
Rosalind
R
Department of Microbiology, University of Washington, Seattle, Washington, USA.
Donaldson
Lara
L
Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa.
Monjane
Adérito L
AL
Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa.
Martin
Darren P
DP
Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
D001483:Base Sequence; D004279:DNA, Viral / Q000032:analysis; D017791:Geminiviridae / Q000235:genetics / Q000302:isolation & purification / Q000472:pathogenicity / Q000502:physiology; D016679:Genome, Viral; D026762:Maize streak virus / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity / Q000502:physiology; D008969:Molecular Sequence Data; D009154:Mutation; D010935:Plant Diseases / Q000821:virology*; D018515:Plant Leaves / Q000821:virology; D011995:Recombination, Genetic; D012641:Selection, Genetic; D003313:Zea mays / Q000821:virology*
D004279:DNA, Viral