title: APOBEC3G and APOBEC3F rarely co-mutate the same HIV genome.
abstract: BACKGROUND
  The human immune proteins APOBEC3G and APOBEC3F (hA3G and hA3F) induce destructive G-to-A changes in the HIV genome, referred to as 'hypermutation'. These two proteins co-express in human cells, co-localize to mRNA processing bodies and might co-package into HIV virions. Therefore they are expected to also co-mutate the HIV genome. Here we investigate the mutational footprints of hA3G and hA3F in a large population of full genome HIV-1 sequences from naturally infected patients to uniquely identify sequences hypermutated by either or both of these proteins. We develop a method of identification based on the representation of hA3G and hA3F target and product motifs that does not require an alignment to a parental/consensus sequence.
  
  
  RESULTS
  Out of nearly 100 hypermutated HIV-1 sequences only one sequence from the HIV-1 outlier group showed clear signatures of co-mutation by both proteins. The remaining sequences were affected by either hA3G or hA3F.
  
  
  CONCLUSIONS
  Using a novel method of identification of HIV sequences hypermutated by the hA3G and hA3F enzymes, we report a very low rate of co-mutation of full-length HIV sequences, and discuss the potential mechanisms underlying this.
authors.affiliation: Centre for Vascular Research, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
authors.forename: Diako
authors.initials: D
authors.lastname: Ebrahimi
authors.forename: Firoz
authors.initials: F
authors.lastname: Anwar
authors.forename: Miles P
authors.initials: MP
authors.lastname: Davenport
mesh_terms: D000071480:APOBEC-3G Deaminase; D003564:Cytidine Deaminase / Q000235:genetics*; D043525:Cytosine Deaminase / Q000235:genetics*; D016679:Genome, Viral; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D009154:Mutation; D059372:Nucleotide Motifs
chemical_list: C492906:APOBEC3F protein, human; D043525:Cytosine Deaminase; D000071480:APOBEC-3G Deaminase; C464924:APOBEC3G protein, human; D003564:Cytidine Deaminase