COMMON MODULAR STRUCTURE OF LENTIVIRUS LTRS

Retroviruses are expressed under the control of viral control regions designated long terminal repeats (LTRs), which contain all signals for transcriptional initiation as well as transcriptional termination. Ho wever, retroviral LTRs from different species within a common genus, s uch as Lentivirus, do not show significant overall sequence homology. We compiled a model of the functional organization of 20 Lentivirus LT Rs which we show to recognize all known Lentivirus LTRs. To this end w e combined our previously published methods for identification of tran scription elements with secondary structure element analysis in a nove l modular approach. We deduced descriptions for three new Lentivirus-s pecific sequence elements present in most of the Lentivirus LTRs but a bsent in LTRs of other retrovirus families (B, C, D-type, BLV-HTLV, Sp uma). Four of the 10 elements defined in our study were primate-specif ic. We were able to deduce a phylogeny based on our model which agrees in general with the phylogeny derived from the polymerase genes of th ese viruses. Our model indicated that more than 100 LTRs from the data bases are of Lentivirus origin and can be clearly separated from all o ther LTR types (B, C, D, BLV-HTLV, Spuma). This selectivity appears to be a unique feature of our modular approach. (C) 1996 Academic Press, Inc.