Splicing regulatory elements within tat exon 2 of human immunodeficiency virus type 1 (HIV-1) are characteristic of group M but not group OHIV-1 strains

In the NL4-3 strain of human immunodeficiency virus type 1 (HIV-1), regulat ory elements responsible for the relative efficiencies of alternative splic ing at the tat, rev, and the env/nef 3' splice sites (A3 through A5) are co ntained within the region of tat exon 2 and its flanking sequences, Two ele ments affecting splicing of tat, rev, and env/nef mRNAs have been localized to this region, First, an exon splicing silencer (ESS2) in NL4-3, located approximately 70 nucleotides downstream from the 3' splice site used to gen erate fat mRNA, acts specifically to inhibit splicing at this splice site. Second, the Mb 3' splice site, which is the most downstream of the three re v 3' splice sites, also serves as an element inhibiting splicing at the env /nef 3' splice site A5. These elements are conserved in some but not all HI V-1 strains, and the effects of these sequence changes on splicing have bee n investigated in cell transfection and in vitro splicing assays. SF2, anot her clade B virus and member of the major (group M) viruses, has several se quence changes within ESS2 and uses a different rev 3' splice site. However , splicing is inhibited by the two elements similarly to NL4-3, As with the NL4-3 strain, the SF2 Mb AG dinucleotide overlaps an A5 branchpoint, and t hus the inhibitory effect may result from competition of the same site for two different splicing factors. The sequence changes in ANT70C, a member of the highly divergent outlier (group O) viruses, are more extensive, and ES S2 activity in fat exon 2 is not present. Group O viruses also lack the rev 3' splice site Mb, which is conserved in all group M viruses, Mutagenesis of the most downstream rev 3' splice site of ANT70C does not increase splic ing at A5, and all of the branchpoints are upstream of the two rev 3' splic e sites, Thus, splicing regulatory elements in tat exon 2 which are charact eristic of most group M HIV-1 strains are not present in group O HIV-1 stra ins.