Polymorphism of the 3′ open reading frame of the virus associated with the acquired immune deficiency syndrome, human T-lymphotropic virus type III

Abstract

The genome of the virus associated with the acquired immune deficiency syndrome (AIDS), human T-lymphotropic virus type III (HTLV-III), includes two open reading frames, not found in other retroviruses. One of these, designated 3' open reading frame (3'orf) is 648 base pairs (bp) in length, and overlaps with the 3' long terminal repeat (LTR) sequences. Sequences of additional HTLV-III clones were determined in order to estimate the level and location of variation within 3'orf, to gain some insight into the function of its protein product. Newly determined sequences are reported for 3'orf of two unintegrated clones of HTLV-III and three cDNA clones made from virion RNA derived from the same cell line infected with pooled blood samples of different patients with AIDS or AIDS-related complex symptoms (ARC). In addition, sequences for 3'orf were derived from an unintegrated viral clone derived from a different cell line infected with a distinct isolate from a single patient. These sequences are compared to those previously reported for six other viral clones. Sequences of 3'orf differ among clones by 1.1-10.4% bp and 2.4-17.0% of predicted amino acids. This represents significantly greater sequence variation than is found in the entire genome on average. Moreover, a functional proviral clone has a termination codon at amino acid residue 124 of this open reading frame. This raises questions concerning the structure, and regulation of expression of the protein encoded by 3'orf.

Production of a non-functional nef protein in human immunodeficiency virus type 1-infected CEM cells

“…The mutated nef protein manifested no changes in its serine residues and it may therefore be considered that the mutation of threonine 15 is the most important of those affecting the phosphorylation sites of the nefprotein. In accord with this, the nef protein of our HIV stock was found to be naturally mutated at threonine 15 into alanine, a substitution which was previously observed in other HIV isolates (Ratner et al, 1985;Alizon et al, 1986;Spire et al, 1989).…”

“…The human immunodeficiency virus (HIV) contains several non-structural proteins which are involved in the regulation of virus infection (Ratner et al, 1985;WainHobson et al, 1985;Guyader et al, 1987). Among these proteins is the product of the nef gene, previously referred to as F, 3' orf, orfB or E'.…”

Highly localized tracks of human immunodeficiency virus type 1 Nef in the nucleus of cells of a human CD4+ T-cell line.

“…Conflicting reports have also been published questioning the role of Nef in each of the above functions (9,36). The issue of the biological function of Nef is further complicated by the fact that isoforms of Nef exist that differ either in the primary amino acid sequence or in their posttranslational modification (37) and these isoforms may have different functions.…”

The 3′‐orf protein of human immunodeficiency virus shows structural homology with the phosphorylation domain of human interleukin‐2 receptor and the ATP‐binding site of the protein kinase family

“…An initial visual search of the deduced amino acid sequences of T-cell receptors IL-2R and T4 (CD4) antigen revealed a stretch of highly charged, mainly basic residues of consensus QRRQ(Xaa)6I, at positions 241-251 of the intracytoplasmic tail of human IL-2R [12,13], showing striking sequence homology (-41%) with a highly charged region (positions 104-114) within the p273'-°rf protein of HIV isolates, located just prior to the premature termination codon found in the 3'-orf sequence of some infectious HIV isolates [8]. As summarized in fig.l, this sequence is highly conserved, with few amino acid changes, among all of the HIV isolates, and has also been identified among a limited but diverse group of proteins, including N-myc [14] and cytochrome P-450 of Pseudomonas putida [15] References cited for HIV isolates: LAV strains BRU, MAL, and ELI [5]; HXB2, HXB3, C15, HAT3, BHI0, BHS, PV22, and SF2 [8]; and CDC451 isolate [38].…”

“…The 3'-orf gene (648 bp) begins in a different reading frame at the end of the gp41 envelope sequence, and extends into the 3'-LTR where it terminates in the U3 region [4][5][6][7]. A premature termination codon (TAG) at position 124 truncates the gene product (124 amino acids) in HIV isolates HX-B2 and BH10 [4,8], whereas most other isolates are predicted to express a protein of 206 amino acids [9,10]. This protein, p273 ,-o~f [9], has been localized to the cytoplasmic fraction of Molt-4 infected [11] and H9-infected ([11], and Samuel, K. Showalter S. and Zweig, M., unpublished) T-cells.…”