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Previous Article | Next Article 
Journal of Virology, February 2001, p. 2014-2018, Vol. 75, No. 4
Department of Veterinary Microbiology and
Pathology, Washington State University, Pullman, Washington
99164-7040
Received 1 September 2000/Accepted 21 November 2000
We recently described a sequence similarity between the small
ruminant lentivirus surface unit glycoprotein (SU) gp135 and the second
conserved region (C2) of the primate lentivirus gp120 which indicates a
structural similarity between gp135 and the inner proximal domain of
the human immunodeficiency virus type 1 gp120 (I. Hötzel and
W. P. Cheevers, Virus Res. 69:47-54, 2000). Here we found that
the seven-amino-acid sequence of the gp120 strand Lentiviruses are a group of strictly
exogenous retroviruses that infect a range of mammalian hosts. One
characteristic of this group of retroviruses is the rapid sequence
divergence observed between virus strains as well as different
lentiviruses, which resulted in the evolution of viruses with large
differences in genome organization and sequence (20). Most
of the sequence homology between highly divergent lentiviruses is
present in the gag and pol gene products
(8, 21). Sequence homology between the envelope
glycoproteins of different lentiviruses has previously been shown
to occur only in the ectodomain of the transmembrane subunit (TM) but
not in the surface unit (SU) glycoprotein (3, 8, 21-23).
Due to this apparent lack of sequence conservation in lentiviral SU, it
has been unclear how the SU of different lentiviruses are structurally
related to each other. To address this question, we recently compared
SU sequences from the gp120 from primate lentiviruses and the
gp135 of small ruminant lentiviruses and found a statistically
significant sequence similarity between the second conserved region
(C2) of gp120 and a 99-amino-acid region from gp135 (10).
Analysis of this gp120-gp135 sequence similarity in the context of the
gp120 structure revealed a partial structural similarity between gp120
and gp135.
The human immunodeficiency virus type 1 (HIV-1) gp120 core bound to CD4
is composed of two major domains, the inner and outer domains, and a
minidomain composed of four antiparallel The most conserved sequences between gp120 and gp135 correspond to
strands Sequence motif of the C5 region of HIV-1 gp120 is present in the SU
of all lentiviruses.
As the sequences of three of the five
0022-538X/01/$04.00+0 DOI: 10.1128/JVI.75.4.2014-2018.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Conservation of Human Immunodeficiency Virus Type 1 gp120 Inner-Domain Sequences in Lentivirus and Type A and B Retrovirus
Envelope Surface Glycoproteins
ABSTRACT
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Abstract
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25 in the C5
region, which is also part of the inner proximal domain, was conserved
in the SU of all lentiviruses in similar or identical positions
relative to the carboxy terminus of SU. Sequences conforming to the
gp135-gp120 consensus for -strand 5 in the C2 region, which is
antiparallel to 25, were then sought in the SU of other lentiviruses
and retroviruses. Except for the feline immunodeficiency virus,
sequences similar to the gp120-gp135 consensus for 5 and part of the
preceding strand 4 were present in the SU of all lentiviruses. This
motif was highly conserved among strains of each lentivirus and
included a strictly conserved cysteine residue in 4. In addition,
the 4/5 consensus motif was also present in the conserved
carboxy-terminal region of all type A and B retroviral envelope surface
glycoproteins analyzed. Thus, the antiparallel -strands 5 and 25 of
gp120 form an SU surface highly conserved among the lentiviruses and at
least partially conserved in the type A and B retroviral envelope glycoproteins.
TEXT
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Abstract
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References
-strands, the bridging
sheet (13). Sequences from the C2 region form most of the
-strands of a two-helix, two-strand bundle and a five-stranded -sandwich in the inner domain as well as some -strands of the outer domain of gp120 (13). Most of the similarity motifs
between gp135 and the C2 region of gp120 coincide with sequences
corresponding to -strands 4 through 8 in the HIV-1 gp120 inner
domain and -strands 11 and 12 in the outer domain (10).
Significantly, all four cysteines that form two disulfide bonds in the
proximal region of the gp120 inner domain as well as the first cysteine
of the gp120 V3 loop in 12 (13, 15) are conserved in
gp135, indicating a partial similarity between the tertiary structures
of gp120 and gp135 (10).
4 and 5 in the five-stranded -sandwich structure of
the proximal region of the inner proximal domain of HIV-1 gp120. Two
additional -strands in this five-stranded -sandwich are derived
from C1 and C5 sequences of HIV-1 gp120 (13). We
hypothesized that C1 and C5 sequences, which are part of a structurally
conserved SU inner proximal domain, should also be conserved between
gp120 and gp135 and possibly in the SU of other lentiviruses. Here we show that two short motifs located in the gp120 C2 and C5 regions which
are part of an antiparallel -sheet in the gp120 inner proximal domain are conserved in the lentiviruses, indicating that a surface of
the inner domain of HIV-1 gp120 is conserved in the SU of other lentiviruses. In addition, the C2 motif is also present in the envelope
glycoproteins encoded by A-type endogenous retroviral elements and type
B retroviruses (type A and B retroviruses), suggesting a local
structural similarity between the SU of lentiviruses and type A and B retroviruses.
-strands of the gp120 inner proximal domain -sandwich are
conserved in gp135, we first tried to determine whether the gp120-gp135
sequence similarity extends to the other two -strands which are part
of this structure. One of these strands is 1, located in the C1
region of gp120 (13). Although the sequence of 1 is
relatively well conserved among the primate lentiviruses, it is only 3 amino acids long, and a reliable assignation of similar sequences in
gp135 could not be done. The other strand of this -sandwich
structure is the 7-amino-acid long 25. This strand is antiparallel
to 5, which is the most conserved sequence between gp120 and gp135
(10, 13). Strand 25 is located about 20 amino acid
residues upstream from the carboxy terminus of HIV-1 gp120 in the C5
region, and its sequence is highly conserved among strains of primate
lentiviruses (sequence KYKVVKI in
HIV-1HXB2; residues conserved between HIV-1 strains are
underlined) (12, 24). The last residue of this motif has
been shown to be important for anchoring of gp120 on gp41
(9), suggesting that 25 is a functionally important
structure of the inner proximal domain of gp120 likely to be conserved
in other lentiviral glycoproteins. Sequences similar to the HIV-1 gp120
25 motif (C5 motif) were visually sought in the gp135
carboxy-terminal region. A similar sequence was found in the caprine
arthritis-encephalitis virus (CAEV) and visna virus gp135 between 33 and 34 amino acid residues upstream from the carboxy terminus of gp135
(Fig. 1B). Similar to the C5 motif
sequence of primate lentiviruses, the gp135 C5 motif is highly
conserved in the gp135 of small ruminant lentiviruses (4, 27, 31,
35, 36). The sequence similarity also included the strictly
conserved residue L483 of HIV-1 gp120 in the preceding 
-helix 5, which is part of the two-helix, two-strand bundle of the inner domain.
Flanking regions of gp120 and gp135 did not show any sequence
similarity (not shown). Due to its short length, the significance of
the conservation of the C5 motif in gp120 and gp135 was unclear. If
this motif is indeed part of a structurally or functionally important
domain of SU and not due only to chance, it should also be conserved in
the SU of other lentiviruses. Therefore, to establish the relevance of
this sequence similarity, we determined whether the C5 motif was also
present in the carboxy terminus of the SU of other lentiviruses.
View larger version (38K):
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FIG. 1.
Alignment of the C2 (A) and C5 (B) motifs of the SU from
lentiviruses and type A and B retroviruses. Numbers at the right of the
alignments indicate the position of the last residue of the motif from
the initiation codon. Letters above the alignment indicate residue
positions within each motif. Black backgrounds represent identical
amino acids or conservative variations between the lentiviruses and
type A and B retroviruses for each position of the motifs. Gray
backgrounds represent identical amino acids or conservative variations
between the lentiviruses and type A and B retroviruses (but which are
nonconservative with the residues in black background) for each
position. Numbers in parentheses indicate the number of amino acids
between the last position of the C5 motif and the carboxy terminus of
SU for each lentivirus. Thick lines indicate sequences which are part
of HIV-1 gp120 strands 4, 5, and 25 and helix 5
(13). HIV-1 and HIV-2, human immunodeficiency virus types
1 (strain HXB2, GenBank accession number K03455) and 2 (strain ROD,
X05291); CAEV, caprine arthritis-encephalitis virus (M33677);
Visna, visna virus (M10608); JSRV, jaagsiekte sheep retrovirus
(M80216); EIAV, equine infectious anemia virus (AF033820); FIV,
feline immunodeficiency virus (M73965); BIV, bovine
immunodeficiency virus (M32690); JDV, jembrana disease lentivirus
(U21603); HERV-K, human endogenous retrovirus K, type 2 genome
(X82272); MMTV, mouse mammary tumor virus (X01811); MIAE, mouse
intracisternal A-type element (M73818).
25 of gp120 is an important structural or functional domain conserved in all lentiviruses.
Sequences similar to an HIV-1 gp120 C2 motif are present in
the SU of most lentiviruses.
Using computer-assisted
searches, we were previously unable to find in EIAV, BIV, or FIV
the same extensive region of similarity that is observed between the C2
region of gp120 and gp135 (10). However, the presence of
the C5 (25) motif in all lentiviruses suggests that sequences
similar to gp120 5, which is antiparallel to 25 and conserved
between gp120 and gp135, are also present in degenerate form in other
lentiviruses. Visual examination of SU sequences from different
lentiviruses revealed the presence of a similar motif (C2 motif) in
EIAV, BIV, and JDV although not in FIV (Fig. 1A). This 12-amino-acid C2
motif encompasses most of gp120 -strands 4 and 5 and includes a
strictly conserved cysteine residue in the 4 region. The C2 motif is
highly conserved between strains of EIAV and BIV. In EIAV, the C2 motif
is stable during persistent infection, with few conservative changes
observed (16, 39). In addition, the C2 motif was found to
be strictly conserved in 176 of 179 EIAV gp90 sequences present in
GenBank, despite considerable sequence variation in other regions.
4/5 region could not be identified in the SU of other
lentiviruses, including the sequence of gp120 8, which has a
cysteine forming a disulfide bond with the conserved 4 cysteine.
Although the C2 motif was not present in FIV gp100, a similar motif was
identified in a location upstream from the FIV gp100 V3 region
(sequence
SYCTDPLQIPLI,
amino acids 318 to 329; conserved residues are underlined), in a
similar relative position from gp100 V3 as the C2 motif from the V3
region of HIV-1 gp120. However, some of the highly conserved positions
of the motif (positions g, h, and j) were not
conserved in FIV gp100, and the significance of this FIV gp100 motif is unclear.
C2 motif is present in type A and B retroviral envelope surface glycoproteins. The conservation of two short motifs in distant regions of SU that are located close to each other in the tertiary structure of HIV-1 gp120 suggests that this region represents a domain of SU that is of structural or functional importance. The TM ectodomains from lentiviruses and type B retroviruses have been shown to have some sequence similarity (19, 34, 38). Therefore, we asked whether sequence similarity between the Env of lentiviruses and type B retroviruses extends to the C2 and C5 motifs of SU.
The type A and B retroviruses have some sequence homology in SU, and most of the sequence homology is located in the carboxy-terminal region of SU (18, 38). Visual examination of SU sequences from the human endogenous retrovirus K (18), mouse intracisternal A-type element (26), the exogenous/endogenous mouse mammary tumor virus (25), and the exogenous/endogenous type B/D jaagsiekte sheep retrovirus (JSRV) and the closely related ovine enzootic nasal tumor virus (which encode type B retroviral envelopes) (6, 38) revealed a sequence closely related to the C2 motif in their conserved carboxy-terminal region (Fig. 1A). This sequence represents one of the most conserved sequences in the SU of this group of retroviruses and is also conserved among different strains or members of endogenous families (not shown). Some positions of the C2 motif, such as positions c, d, and g, are strictly or almost completely conserved between the lentiviruses and type A and B retroviruses. However, more informative than the sequence similarity between lentiviruses and type A and B retroviruses is the lack of distinction between the patterns of sequence variation for each position of the motif within and between retrovirus groups, even between closely related viruses. For example, position e of the C2 motif within both the lentiviruses and type A and B retroviruses can be either Pro or basic/Gln; the "dimorphic" position f encodes only Tyr/Trp or Pro (except in HIV-1); position h encodes either Phe or Tyr in all sequences; position i encodes either Ala or a hydrophobic residue in most sequences; position j encodes either Ile, Leu, or Phe in all sequences; position k encodes either Leu, Ile, or Val in all sequences; and position l is preferentially Lys, Arg, or Gln in the lentiviruses and JSRV. Most of these degenerate positions represent very conservative variations (positions a and h through l) or a restricted number of nonconservative variations (positions e and f, in the turn between4 and 5). The sequence conservation and common pattern of variation between the C2 motifs of
lentiviruses and type A and B retroviruses indicate a similar structural or functional constraint on sequence variation in the SU of
these two groups of viruses.
In contrast to the type A and B retroviruses, sequences similar to the
C2 or C5 motifs could not be found in the SU of the Moloney murine
leukemia virus, bovine leukemia virus, human T-cell leukemia virus
types 1 and 2 (HTLV-1 and HTLV-2), Rous sarcoma virus, feline RD114
endogenous retrovirus, baboon endogenous retrovirus, feline leukemia
virus type A, the Mason-Pfizer monkey retrovirus, or any
spumaretrovirus even when using the Findpatterns program of the GCG
package (7).
Here we show that two short SU motifs are highly conserved in the
lentiviruses and that one of these motifs is also conserved in the type
A and B retroviruses. Many of the pairwise alignments were not
statistically significant when tested by the Monte Carlo simulation of
the Bestfit program of the GCG package and could therefore be
attributed to chance. However, when all lentiviral sequences are
included in the analysis and the multiple alignment is interpreted in
the context of the X-ray structure of HIV-1 gp120, the conserved C2 and
C5 motifs have a clear structural significance. The conservation of
these motifs indicates that the region of the HIV-1 gp120 inner
proximal domain centered on the antiparallel -strands 5 and 25 forms
a highly conserved lentiviral SU surface and suggests a possible
structural similarity between the SU of lentiviruses and type A and B
retroviruses in that domain. Although the C2 motif is too short to rule
out convergent evolution between the SU of lentiviruses and type A and
B retroviruses, their sequence similarity in TM (19, 34,
38) supports a common origin for most or the entire
env genes of these two retroviral groups.
The reason for the disagreement between the different degrees of
sequence similarity in the SU of lentiviruses and the phylogenetic analyses of the pol gene products is unclear but probably
reflects differences in evolutionary rates in different lentiviruses or recombination events (19, 20). Precedents for
recombination events between env genes of closely or
distantly related retroviruses, deduced from phylogenetic analyses,
have been described. An exchange of env sequences probably
occurred between HTLV-1 and HTLV-2 (19) and between a type
C retrovirus closely related to the avian reticuloendotheliosis virus
and a type B retrovirus which originated the type D retroviruses (19, 38).
Modeling of the trimeric SU complex on the virion surface indicates
that strands 5 and 25 form part of the most virion-proximal surface of the gp120 core (14, 37). While none of the
residues of the C2 motif was directly tested for interactions with TM, at least one of the residues of 25 in the C5 region of HIV-1 gp120,
I491, is important for stable SU-TM interactions (9). Therefore, the conserved lentiviral SU surface may represent a common
structure among lentiviruses and possibly type A and B retroviruses for
anchoring SU on TM in the envelope glycoprotein complex. It is
interesting that the C5 motif region, which forms a -strand in the
CD4-bound gp120 core, is included in a computer-modeled pocket
structure postulated to be important in SU-TM interactions (28), suggesting a structural basis for SU shedding upon
receptor-induced conformational change.
The sequence of the HIV-1 gp120 outer domain, shown as a cross-hatched
box in Fig. 2, is included entirely
between the C2 and C5 motifs (13). Our previous sequence
analysis indicates that the gp135s of small ruminant lentiviruses have
a similar inner/outer domain organization: most strands of the inner
domain -sandwich as well as 12, located in the outer domain
immediately upstream from the gp120 V3 loop, are conserved between
gp135 and the gp120 of primate lentiviruses (10). The
identification of a homologue of gp120 25 in gp135 about 290 amino
acid residues downstream from the C2 motif provides further support for
a similar domain organization in the SU of primate and small ruminant
lentiviruses. Consistent with this interpretation, the putative outer
domain of gp135, located between the C2 and C5 motifs, is highly
glycosylated and contains more than 80% of the potential N-linked
glycosylation sites of gp135 (11), similar to the heavy
glycosylation of the gp120 outer domain (37). In this
gp135 domain model, the distance between the C2 and C5 motifs in the
primary structure of SU would indicate a larger relative size of the
putative outer domain of gp135 than gp120 outer domain. The presence of
the C2 and C5 motifs in EIAV, BIV, and JDV would also suggest an
analogous inner/outer domain organization for the SU of these
lentiviruses. However, the shorter sequence between the C2 and C5
motifs in EIAV, BIV, and JDV may indicate either a much smaller or
absent outer domain in the SU of these viruses (Fig. 2). The conserved
C2 motif of EIAV gp90 was shown to be part of a minor neutralization
epitope recognized by a murine monoclonal antibody (1),
suggesting that the EIAV C2 motif is better exposed on the virion
surface than the C2 motif of gp120, compatible with a smaller or
absent outer domain in gp90. Interestingly, the C2 motif of type A and B retroviruses is located in the carboxy terminus of SU (Fig. 2) and C5
appears to be absent, indicating that the surface glycoproteins of type
A and B retroviruses, although possibly structurally related to the SU
of lentiviruses, probably lack an outer domain homologue and have a
different domain organization than the SU of lentiviruses.
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ACKNOWLEDGMENTS |
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This work was supported by NIH grants RO1 AR 43718 and R21 AI 42690.
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FOOTNOTES |
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* Corresponding author. Mailing address: Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164-7040. Phone: (509) 335-6072. Fax: (509) 335-8529. E-mail: ihe{at}vetmed.wsu.edu.
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