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Journal of Virology, December 2002, p. 12360-12364, Vol. 76, No. 23
0022-538X/02/$04.00+0 DOI: 10.1128/JVI.76.23.12360-12364.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
T-Cell Receptor:CD3 Down-Regulation Is a Selected In Vivo Function of Simian Immunodeficiency Virus Nef but Is Not Sufficient for Effective Viral Replication in Rhesus Macaques
Jan Münch,1 Ajit Janardhan,2,3 Nicole Stolte,4 Christiane Stahl-Hennig,4 Peter ten Haaft,5 Jonathan L. Heeney,5 Tomek Swigut,3 Frank Kirchhoff,1* and Jacek Skowronski3*
Abteilung Virologie, Universitätsklinikum, 89081 Ulm, Germany,1
Program in Genetics, State University of New York at Stony Brook, Stony Brook, New York 11794,2
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724,3
German Primate Center, 37077 Göttingen, Germany,4
Department of Virology, Biomedical Primate Research Center, 2288 GJ Rijswijk, The Netherlands5
Received 8 April 2002/
Accepted 26 August 2002

ABSTRACT
We investigated the function of severely truncated simian immunodeficiency
virus (SIV) Nef proteins (tNef) in vitro and in vivo. These
variants emerged in rhesus monkeys infected with SIVmac239 containing
a 152-bp deletion in the
nef-unique region and have been suggested
to enhance SIV virulence (E. T. Sawai, M. S. Hamza, M. Ye, K.
E. Shaw, and P. A. Luciw, J. Virol. 74:2038-2045, 2000). We
found that the tNef proteins were unable to down-regulate the
cell surface expression of major histocompatibility complex
class I proteins, CD4, and CD28 and neither stimulated SIV replication
nor enhanced virion infectivity. The tNef proteins did efficiently
down-regulate T-cell receptor (TCR):CD3 cell surface expression.
Nevertheless, the SIVmac239
tnef variants were strongly attenuated
in six infected juvenile rhesus macaques. Thus, while the ability
of SIV Nef to down-modulate TCR:CD3 cell surface expression
apparently confers a selective advantage in vivo, it is insufficient
for efficient viral replication in infected macaques. Additional
mutations elsewhere in SIVmac239
tnef genomes are required for
a virulent phenotype.

TEXT
The 792-bp
nef gene of the pathogenic simian immunodeficiency
virus mac239 clone (SIVmac239) encodes a myristylated protein
of approximately 34 kDa that down-regulates the cell surface
expression of CD3, CD4, CD28, and major histocompatibility class
I (MHC-I) molecules, enhances viral replication, increases the
infectivity of viral particles, and associates with the p21-regulated
protein serine kinase PAK2 (
10-
13,
16,
17,
23-
25). These multiple
functions of 239wt Nef are genetically separable and require
distinct elements located throughout the Nef molecule.
Nef is important for efficient viral replication and the persistence of HIV and SIV in vivo (7, 13-15). Adult or juvenile rhesus macaques inoculated with a variant of the pathogenic SIVmac239 clone containing a deletion of 182 bp in the nef gene (nef
182) (Fig. 1) usually exhibit low viral loads, and the majority of infected animals do not progress to immunodeficiency (13). These results provided the basis for the design and evaluation of live attenuated SIV vaccines with deletions in accessory genes (6).
Recently, it was found that uncloned SIVmac239 variants expressing
truncated Nef (tNef) proteins of about 25 kDa are pathogenic
in infected rhesus macaques (
20). These variants emerged in
animals infected with recombinant SIVmac239 viruses containing
a missense mutation of the Nef initiator methionine, combined
with either a 152-bp deletion in the
nef-unique region or an
insertion of the interleukin-2 (IL-2) cDNA in place of the 152-bp
deletion, both of which introduced frameshifts into the
nef open reading frame (ORF) (Fig.
1). In the reverted
tnef alleles,
the
nef ATG initiation codon was restored and frameshift mutations
were repaired to restore contiguous, albeit truncated,
nef ORFs
(
tnef24 and
tnef46) (Fig.
1) (
20). The tNef proteins lack an
approximately 50-amino-acid-long region overlapping the highly
conserved core of the Nef protein. This deletion spans elements
mediating functional interactions of Nef with clathrin adaptor
complexes that are required for the down-regulation of CD4 and
CD28, as well as elements required for Nef to associate with
PAK2 activity (
4,
16,
18). Therefore, it was surprising that
the tNef proteins were linked to a pathogenic phenotype.
The emergence of variant viruses containing a restored tnef ORF indicated that the severely truncated tNef proteins (tNef24 and tNef46) contained some residual function. To identify this function, we constructed truncated 239nef alleles, tnef.1 and tnef.2, corresponding to those previously recovered from the progressing animals 29810-24 and 27021-46N, respectively (20). The mutant tnef.1 and tnef.2 alleles were generated by splice overlap extension PCR and cloned into both a bicistronic vector coexpressing GFP (pCGCG.tNef.1 and pCGCG.tNef.2) and a proviral SIVmac239 construct essentially as described previously (12, 19). Flow cytometry analysis of Jurkat T cells transiently transfected with the bicistronic vectors (9, 11, 12) revealed that, in contrast to 239wt Nef, the tNef.1 and tNef.2 proteins did not decrease the cell surface expression of CD4, CD28, and MHC-I molecules (Fig. 2) (data not shown). However, both tNef forms down-regulated the cell surface expression of the T-cell receptor (TCR):CD3 complex as efficiently as 239wt Nef (Fig. 2) (data not shown). Down-modulation of TCR:CD3 is a conserved function of SIVmac239 and HIV-2 Nef proteins (2, 10, 21).
To test the ability of the tNefs to stimulate SIV replication
and particle infectivity, virus stocks were generated in 239T
cells transiently transfected with the respective wild-type
and mutant proviral genomes (
8). As expected (
16), no significant
differences in the replication kinetics of SIVmac239 viruses
containing the 239wt
nef,
tnef.1, and
tnef.2 alleles were observed
in CEMx174 cells (Fig.
3A). Western blot analysis revealed that
CEMx174 cells infected with the SIVmac239 variants expressed
tNef proteins of the expected size of about 25 kDa (data not
shown). Infection of rhesus macaque peripheral blood mononuclear
cells (rhPBMC) (Fig.
3B) and the herpesvirus saimiri
-transformed
macaque T-cell line 221 (Fig.
3C) (
1) demonstrated that, in
contrast to the 239wt
nef allele, the
tnef.1 and
tnef.2 alleles
were unable to stimulate SIVmac239 replication. Additionally,
the tNef proteins did not increase virion infectivity (Fig.
3D).
Of the six in vitro Nef activities investigated, the only one
retained by the tNef proteins was the ability to down-regulate
TCR:CD3. Therefore, the previous suggestion that the severely
truncated tNef proteins were capable of significantly increasing
SIV virulence in rhesus macaques was surprising (
20). However,
in this study, virus was recovered from the progressing animal,
26939-105N, near necropsy, leaving the possibility that mutations
elsewhere in the viral genome might have contributed to the
virulent phenotype.
To address this possibility, six juvenile rhesus macaques were inoculated intravenously with SIVmac239 tnef.1 virus stock containing 5 ng of p27 produced from transiently transfected 293T cells as described previously (8). The animals were healthy and seronegative for SIV, D-type retroviruses, and STLV-1 at the time of infection. Sera and PBMCs were collected from the infected rhesus monkeys at regular intervals. Serological, virological, and immunological analyses of the clinical samples were performed as described before (22, 23, 26). As shown in Fig. 4, following initial spikes in the acute phase, the viral RNA copy numbers and cell associated viral loads were low in all six animals infected with SIVmac239 tnef.1 compared to those infected with wild-type SIVmac239. In agreement with the observed attenuated in vivo replication of SIVmac239 tnef.1, the total CD4+ T cells and CD4+ CD29+ memory T cells were essentially unchanged in the infected animals (Fig. 5), all of whom remained healthy throughout the 40-week observation period. Thus, the SIVmac239 tnef.1 allele was severely attenuated, and the infections were well controlled in all animals.
Intact but truncated
tnef ORFs were independently restored in
several animals infected with SIVmac239 variants containing
the 152-bp deletion (
20), yet this was never observed in macaques
infected with an SIVmac239 variant containing a 182-bp deletion
(
13,
14). Both deletions start at nucleotide position 172 of
the
nef ORF (
13,
20). However, in contrast to the 152-bp deletion,
the 182-bp deletion removes nucleotides encoding amino acids
111 to 120 of the Nef protein (see Fig.
1). This suggested that
amino acids 111 to 120 might be required to down-regulate TCR:CD3
cell surface expression. To address this possibility, the frameshift
mutations introduced by the 152- and 182-bp deletions were repaired
by removing an additional single nucleotide in the respective
nef ORFs. The resulting
nef variants (
nef
153 and
nef
183, see
Fig.
1) were expressed transiently in Jurkat T cells. As shown
in Fig.
6, Nef
153 down-modulated the cell surface expression
of TCR:CD3. In contrast, Nef
183 was not able to down-modulate
TCR:CD3 (Fig.
6), and was also defective in all other in vitro
assays of Nef functions tested (data not shown). Thus, a selective
pressure for TCR:CD3 down-regulation may explain why the truncated
Nef proteins emerged only in animals infected with SIVmac239
containing the 152-bp deletion in the
nef-unique region. This
event was not possible in animals infected with SIVmac239 containing
the 182-bp deletion because it removed amino acids required
for TCR:CD3 downregulation.
In summary, there are two novel implications of this work. First,
it is evident that TCR:CD3 down-regulation by SIVmac239 Nef
is associated with a selective advantage for the virus in vivo.
However, this function alone is insufficient for high viral
loads and rapid disease induction by SIVmac239 in infected rhesus
macaques. This is consistent with recent evidence suggesting
that a combination of several independent Nef functions allows
SIVmac239 and HIV-1 to replicate efficiently in the infected
host (
3,
5,
12,
19). Second, our data imply that changes elsewhere
in the viral genome are required for a pathogenic phenotype
of SIVmac239 expressing the tNef proteins. It will be important
to determine the nature of such alterations in the SIVmac genome
that can compensate for the loss of other Nef functions.

ACKNOWLEDGMENTS
We thank Mandy Krumbiegel and Nathaly Finze for excellent technical
assistance and Ingrid Bennett for critical reading of the manuscript.
We also thank Thomas Mertens and Bernhard Fleckenstein for constant
support and encouragement.
This work was supported by grants from the Wilhelm-Sander Foundation and the Deutsche Forschungsgemeinschaft (to F.K.), as well as the Public Health Service (AI-42561 to J.S.).

FOOTNOTES
* Mailing address for Frank Kirchhoff: Abteilung Virologie-Universit@auml;tsklinikum, Albert-Einstein-Allee 11, 89081 Ulm, Germany. Phone: 49 (731) 50023344. Fax: 49 (731) 50023389. E-mail:
frank.kirchhoff{at}medizin.uni-ulm.de.

Corresponding author. Mailing address for Jacek Skowronski: Cold Spring Harbor Laboratory, 1 Bungtown Rd., Cold Spring Harbor, NY 11724. Phone: (516) 367-8407. Fax: (516) 367-8454. E-mail: skowrons{at}cshl.org. 

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Journal of Virology, December 2002, p. 12360-12364, Vol. 76, No. 23
0022-538X/02/$04.00+0 DOI: 10.1128/JVI.76.23.12360-12364.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
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