Complex Recombination Patterns Arising during Geminivirus Coinfections Preserve and Demarcate Biologically Important Intra-Genome Interaction Networks

PLoS Pathogens

Jean-Yves Semegni¹  Jean-Michel Lett²  Arvind Varsani²  Claire Vincent²  Darren P. Martin³  Pierre Lefeuvre³  Bernard Reynaud³  Betty Dijoux⁴  Murielle Hoareau⁵ 

[1] Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand;CIRAD, UMR 53 PVBMT CIRAD-Université de la Réunion, Pôle de Protection des Plantes, Ligne Paradis, Saint Pierre, La Réunion, France;Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, South Africa;Electron Microscope Unit, University of Cape Town, Rondebosch, Cape Town, South Africa;School of Biological Sciences, University of Canterbury, Christchurch, New Zealand

关键词: Recombinant proteins;    DNA recombination;    Protein interactions;    Viral genomics;    Genomic imprinting;    Structural genomics;    Protein-protein interactions;    Viral structure;   

DOI  :  10.1371/journal.ppat.1002203

学科分类：生物科学（综合）

来源: Public Library of Science

【 摘 要 】

Genetic recombination is an important process during the evolution of many virus species and occurs particularly frequently amongst begomoviruses in the single stranded DNA virus family, Geminiviridae. As in many other recombining viruses it is apparent that non-random recombination breakpoint distributions observable within begomovirus genomes sampled from nature are the product of variations both in basal recombination rates across genomes and in the over-all viability of different recombinant genomes. Whereas factors influencing basal recombination rates might include local degrees of sequence similarity between recombining genomes, nucleic acid secondary structures and genomic sensitivity to nuclease attack or breakage, the viability of recombinant genomes could be influenced by the degree to which their co-evolved protein-protein and protein-nucleotide and nucleotide-nucleotide interactions are disreputable by recombination. Here we investigate patterns of recombination that occur over 120 day long experimental infections of tomato plants with the begomoviruses Tomato yellow leaf curl virus and Tomato leaf curl Comoros virus. We show that patterns of sequence exchange between these viruses can be extraordinarily complex and present clear evidence that factors such as local degrees of sequence similarity but not genomic secondary structure strongly influence where recombination breakpoints occur. It is also apparent from our experiment that over-all patterns of recombination are strongly influenced by selection against individual recombinants displaying disrupted intra-genomic interactions such as those required for proper protein and nucleic acid folding. Crucially, we find that selection favoring the preservation of co-evolved longer-range protein-protein and protein DNA interactions is so strong that its imprint can even be used to identify the exact sequence tracts involved in these interactions.

【 授权许可】

CC BY