A new role for HIV nucleocapsid protein in modulating the specificity of plus strand priming

The current study indicates a new role for HIV nucleocapsid protein (NC) in modulating the specificity of plus strand priming. RNase H cleavage by reverse transcriptase (RT) during minus strand synthesis gives rise to RNA fragments that could potentially be used as primers for synthesis of the plus strand, leading to the initiation of priming from multiple points as has been observed for other retroviruses. For HIV, the central and 3′ polypurine tracts (PPTs) are the major sites of plus strand initiation. Using reconstituted in vitro assays, results showed that NC greatly reduced the efficiency of extension of non-PPT RNA primers, but not PPT. Experiments mimicking HIV replication showed that RT generated and used both PPT and non-PPT RNAs to initiate “plus strand” synthesis, but non-PPT usage was strongly inhibited by NC. The results support a role for NC in specifying primer usage during plus strand synthesis.