Figure 2

Phenotypic capsid-nucleocapsid differences of the gag polyprotein based on the three classes. Retroviridae differentiation into 3 previously proposed classes suggests how vertebrate retroviruses code for 3 different gag polyproteins, based on the CA-NC region. A) Sequence logo describing the CA-NC region coded by all gamma- and epsilonretroviruses (class I) used in this study. Class I gag exhibits several features (underlined in the Figure) the presence of a single CCHC array at NC being the most prominent. B) Sequence logo describing the class II CA-NC region was built on an alignment including lentiviral (HIV-1, HIV-2, SIVMAC, VMV, SA-OMVV and CAEV), betaretroviral (MPMV, SERV and SRV-1), alpharetroviral (LPDV and RSV), and deltaretroviral (HTLV-1, HTLV-2 and BLV) sequences. Class II gag amino acidic architecture is similar but displays important differences from that of class I. Note, for instance, how the C-terminus of class II gag is based on a trait we call "NAN-C-C-KA-P" followed by 2 CCHC arrays at NC. C) Sequence logo constructed based on all class III gags used. Class III gag has a CA trait extremely dissimilar from those of classes I and II. On the other hand, class III NC equivalent trait is rich on residues having similar physiochemical properties to those displayed in class I, but have no CCHC arrays.