Organisation of HIV

Different Mutagenic Potential of HIV-1 Restriction Factors APOBEC3G and APOBEC3F Is Determined by Distinct Single-Stranded DNA Scanning Mechanisms.

• Abstract
  
  The APOBEC3 deoxycytidine deaminase family functions as host restriction factors that can block replication of Vif (virus infectivity factor) deficient HIV-1 virions to differing degrees by deaminating cytosines to uracils in single-stranded (−)HIV-1 DNA. Upon replication of the (−)DNA to (+)DNA, the HIV-1 reverse transcriptase incorporates adenines opposite the uracils, thereby inducing C/G→T/A mutations that can functionally inactivate HIV-1. Although both APOBEC3F and APOBEC3G are expressed in cell types HIV-1 infects and are suppressed by Vif, there has been no prior biochemical analysis of APOBEC3F, in contrast to APOBEC3G. Using synthetic DNA substrates, we characterized APOBEC3F and found that similar to APOBEC3G; it is a processive enzyme and can deaminate at least two cytosines in a single enzyme-substrate encounter. However, APOBEC3F scanning movement is distinct from APOBEC3G, and relies on jumping rather than both jumping and sliding. APOBEC3F jumping movements were also different from APOBEC3G. The lack of sliding movement from APOBEC3F is due to an ¹⁹⁰NPM¹⁹² motif, since insertion of this motif into APOBEC3G decreases its sliding movements. The APOBEC3G NPM mutant induced significantly less mutations in comparison to wild-type APOBEC3G in an in vitro model HIV-1 replication assay and single-cycle infectivity assay, indicating that differences in DNA scanning were relevant to restriction of HIV-1. Conversely, mutation of the APOBEC3F ¹⁹¹Pro to ¹⁹¹Gly enables APOBEC3F sliding movements to occur. Although APOBEC3F ¹⁹⁰NGM¹⁹² could slide, the enzyme did not induce more mutagenesis than wild-type APOBEC3F, demonstrating that the unique jumping mechanism of APOBEC3F abrogates the influence of sliding on mutagenesis. Overall, we demonstrate key differences in the impact of APOBEC3F- and APOBEC3G-induced mutagenesis on HIV-1 that supports a model in which both the processive DNA scanning mechanism and preferred deamination motif (APOBEC3F, 5′TTC; APOBEC3G 5′CCC) influences the mutagenic and gene inactivation potential of an APOBEC3 enzyme.

  
  

  Author Summary

  
  Human cells possess a family of seven DNA-modification enzymes, termed APOBEC3, that function as part of our innate immune system. The enzymes modify cytosine in DNA which induces mutations. There are particular enzymes, APOBEC3D, APOBEC3F, APOBEC3G and APOBEC3H, that appear to be most relevant to restricting HIV-1 replication in CD4+ T cells using this mutagenic mechanism, if they can avoid degradation that is induced by the HIV-1 protein Vif. There has been little biochemical analysis of APOBEC3 enzymes other than APOBEC3G in terms of the mechanism by which these enzymes search DNA for target cytosines to deaminate. We conducted a biochemical analysis of APOBEC3F. We found that while APOBEC3G uses 1-dimensional sliding and 3-dimensional translocations, APOBEC3F is restricted to 3-dimensional translocations. This makes the searching mechanism of APOBEC3F superficial and detrimental to the induction of a large number of mutations. In addition, gene inactivation was less likely to occur upon deamination of the target motif of APOBEC3F (5′TTC), in comparison to the target motif of APOBEC3G (5′CCC). All together the data support a model in which the way these enzymes scan DNA can predict the magnitude of mutagenesis induced and the target motif can predict ability to cause gene inactivation.

  Citation: Rakesh ranjan(2018) Different Mutagenic Potential of HIV-1 Restriction Factors APOBEC3G and APOBEC3F Is Determined by Distinct Single-Stranded DNA Scanning Mechanisms.
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