Analysis of human immunodeficiency virus type 1 nef gene sequences present in vivo

Abstract

The nefgenes of the human immunodeficiency viruses type 1 and 2 (HIV-1 and HIV-2) and the related simian immunodeficiency viruses (SIVs) encode a protein (Nef) whose role in virus replication and cytopathicity remains uncertain. As an attempt to elucidate the function of nef, we characterized the nucleotide and corresponding protein sequences of naturally occurring nef genes obtained from several HIV-1-infected individuals. A consensus Nef sequence was derived and used to identify several features that were highly conserved among the Nef sequences. These features included a nearly invariant myristylation signal, regions of sequence polymorphism and variable duplication, a region with an acidic charge, a (PXX)4 repeat sequence, and a potential protein kinase C phosphorylation site. Clustering of premature stop codons at position 124 was noted in 6 of the 54 Nef sequences. Further analysis revealed four stretches of residues that were highly conserved not only among the patient-derived HIV-1 Nef sequences, but also among the Nef sequences of HIV-2 and the SIVs, suggesting that Nef proteins expressed by these retroviruses are functionally equivalent. The "Nef-defining" sequences were used to evaluate the sequence alignments of known proteins reported to share sequence similarity with Nef sequences and to conduct additional computer-based searches for similar protein sequences. A gene encoding the consensus Nef sequence was also generated. This gene encodes a full-length Nef protein that should be a valuable tool in further studies of Nef function.

Association of Human Immunodeficiency Virus Nef Protein with Actin is Myristoylation Dependent and Influences its Subcellular Localization

“…Although this SH3-binding region is also well conserved in HIV-2 Nef, HIV-1 and HIV-2 Nef differ in the residues following the PXXP motif. In HIV-1 Nef, amino acids 84-86 (YKA) are highly conserved and part of a putative protein kinase C (PKC) site [50]. Both HIV-2 Nef proteins used in this study share the sequence FRL at this position (amino acids 112-114 in HIV-2 Nef) therefore lacking the putative PKC site.…”

Refined solution structure and backbone dynamics of HIV‐1 Nef

“…The internal mobility of this region reaches a maximum at residues V66 and G67 with NOEs of -0.2 and T2 values 2140 ms. This mobile region, which also is characterized by fast amide proton exchange, corresponds to a highly conserved acidic region in the Nef primary sequence (Shugars et al, 1993).…”

“…It was previously shown (Grzesiek et al, 1996a) that the regions of defined secondary structure in Nef correspond to highly conserved contiguous sets of amino acids in sequences derived from HIV-1, HW-2, and primate lentiviruses isolates (Shugars et al, 1993). In contrast, only a relatively small subset of noncontiguous residues in the V148-Vl80 loop region is highly (295% identity) conserved, i.e., V148, E154, A156, E160, L164, L165, H166, P167, H171, G172, and Dl75 (Shugars et al, 1993). However, the length of this loop (-30 amino acids) is remarkably well preserved (Shugars et al, 1993).…”

“…In contrast, only a relatively small subset of noncontiguous residues in the V148-Vl80 loop region is highly (295% identity) conserved, i.e., V148, E154, A156, E160, L164, L165, H166, P167, H171, G172, and Dl75 (Shugars et al, 1993). However, the length of this loop (-30 amino acids) is remarkably well preserved (Shugars et al, 1993). Although this loop is not structured in the previously described complexes of Nef, it might be involved in the interaction with another as yet unidentified ligand.…”

“…This latter activity of Nef is linked to a conserved polyproline repeat from residues 69-78 (Goldsmith et al, 1995;Saksela et al, 1995). The polyproline motif is reminiscent of an SH3 target site (Shugars et al, 1993;Saksela et al, 1995), and Nef has been shown to bind specifically and with sub-micromolar affinity to the SH3 domains of a subset of Src family kinases (Lee et al, 1995(Lee et al, , 1996Saksela et al, 1995).…”