Partial “Repair” of DefectiveNEFGenes in a Long‐Term Nonprogressor with Human Immunodeficiency Virus Type 1 Infection

Abstract

A 36-bp deletion close to the 5' end of NEF that impaired Nef function was found in a long-term nonprogressor with human immunodeficiency virus type 1 (HIV-1) infection. Forms containing an adjacent duplication of 33 bp were also frequently observed. The duplication showed no homology to the deleted region but restored the overall length of the first variable loop of Nef. NEF alleles carrying the duplication were active in class I major histocompatibility complex (MHC-I) down-modulation and enhancement of virus infectivity. However, they showed little activity in CD4 down-regulation and were unable to stimulate viral replication in human peripheral blood mononuclear cells. Our study indicates that the enhancement of virion infectivity and the stimulation of HIV-1 replication in lymphocytes are distinct functions of Nef. Our findings also illustrate the capacity for repair of attenuating deletions in HIV-1 infection and suggest that a selective pressure for Nef-mediated MHC-I down-modulation and/or enhancement of virion infectivity exists.

Enhanced CD4 Down-modulation by Late Stage HIV-1 nef Alleles Is Associated with Increased Env Incorporation and Viral Replication

“…Supernatants were collected at regular intervals, and virus production was measured by reverse transcriptase (RT) assay. The radioactivity level present in each dot was quantitated as photo-stimulated luminescence (PSL) by using a Fuji BAS1000 phosphorimaging device as described elsewhere (50).…”

Interactions of HIV-1 NEF with cellular signal transducing proteins

“…It remains to be examined if a similar auto/paracrine effect also explains the enhanced replicative kinetics observed for Nef(+) viruses (HIV and SIV) in suboptimally stimulated primary cell cultures, a Nef function that appears to be distinct from its ability to increase HIV particle infectivity (92).…”

“…These have been suggested to involve the SH2 domain of Lck (81,123) and/or additional bridging proteins (121). Second, while binding of Nef to the SH3 domain of Hck results in efficient activation of its catalytic function (92,114), as predicted based on the structural design of the Src kinases (115,116), it has been reported that Nef inhibits the catalytic activity of Lck (81,82). Third, Nef was reported to become tyrosine phosphorylated by Lck (81,121), whereas Nef was not found to be a substrate for tyrosine phosphorylation by Hck even though its kinase activity is strongly activated upon binding to Nef (92,114).…”

“…Second, while binding of Nef to the SH3 domain of Hck results in efficient activation of its catalytic function (92,114), as predicted based on the structural design of the Src kinases (115,116), it has been reported that Nef inhibits the catalytic activity of Lck (81,82). Third, Nef was reported to become tyrosine phosphorylated by Lck (81,121), whereas Nef was not found to be a substrate for tyrosine phosphorylation by Hck even though its kinase activity is strongly activated upon binding to Nef (92,114). Thus, if Hck and Lck both turn out to be important mediators of Nef function, despite their extensive structural and functional homology they appear to do so by very different molecular mechanisms,…”

Inefficient Enhancement of Viral Infectivity and CD4 Downregulation by Human Immunodeficiency Virus Type 1 Nef from Japanese Long-Term Nonprogressors

“…Thus, reporter cells including HeLa-CD4-LTR-␤Gal cells (MAGI) (27) are often preferred for analysis. In assays using reporter cells, the difference in infectivity between the nefdefective mutant and wild-type HIV is less than 10-fold in most cases (2,3,7,11,25). Considering a large statistical error in the infectivity assay, this difference seems to be subtle.…”