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Journal of Virology, March 2000, p. 2067-2072, Vol. 74, No. 5
Friedrich Miescher-Institut, CH-4002 Basel,
Switzerland
Received 18 June 1999/Accepted 2 December 1999
Using the yeast three-hybrid system, the interaction of the
Cauliflower mosaic virus (CaMV) pregenomic 35S RNA (pgRNA)
leader with the viral coat protein, its precursor, and a series of
derivatives was studied. The purine-rich domain in the center of the
pgRNA leader was found to specifically interact with the coat protein. The zinc finger motif of the coat protein and the preceding basic domain were essential for this interaction. Removal of the N-terminal portion of the basic domain led to loss of specificity but did not
affect the strength of the interaction. Mutations of the zinc finger
motif abolished not only the interaction with the RNA but also viral
infectivity. In the presence of the very acidic C-terminal domain,
which is part of the preprotein but is not present in the mature CP,
the interaction with the RNA was undetectable.
Cauliflower mosaic virus
(CaMV) (Fig. 1) is the type member of the
caulimoviruses, which, together with the animal hepadnaviruses and the
plant badnaviruses, are classified as pararetroviruses. Pararetroviruses, retroviruses, and retrotransposons form the group of
retroelements (25). Foamy viruses are intermediate between
pararetroviruses and retroviruses (32). Two important features distinguish pararetroviruses from retroviruses. First, mature
pararetrovirus particles contain a double-stranded DNA genome while
retroviruses contain two copies of an RNA genome. Second, in
retroviruses the DNA is integrated into the host genome and in
pararetroviruses it remains as multiple copies of a circular minichromosome. However, both forms of viral DNA direct the production of terminally redundant RNA, which plays a dual role as a replicative intermediate and as mRNA (for a review, see reference
40).
0022-538X/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
Interaction of the Cauliflower Mosaic Virus Coat
Protein with the Pregenomic RNA Leader


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ABSTRACT
Top
Abstract
Introduction
Materials and Methods
Results
Discussion
References
![]()
INTRODUCTION
Top
Abstract
Introduction
Materials and Methods
Results
Discussion
References

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FIG. 1.
(A) The genomic map of CaMV DNA is represented by a thin
double line, with the box marked R' indicating the region of the genome
which is transcribed twice in the terminally redundant transcript. The
major viral transcript, 35S RNA (pgRNA), is shown as a thin arrow
inside the DNA. The thick arrows outside the DNA represent the major
viral ORFs: ORF VII (unknown function), ORF I (movement protein), ORF
II (aphid transmission factor), ORF III (DNA binding protein, perhaps
playing a role in nucleic acid condensation during assembly), ORF IV
(capsid protein), ORF V (protease and reverse transcriptase), and ORF
VI (inclusion body matrix protein; translational transactivator).
(Redrawn from reference 40.) (B) Secondary structure
of the CaMV 35S RNA leader (Strasbourg strain). The plot represents the
most stable secondary structure predicted by the program MFOLD at
25°C. The boundaries of the conserved purine-rich sequence are
indicated by arrowheads. Numbers delimit the central part of the leader
used in this study.
The mechanism used by CaMV to package its genome remains unclear. It is likely that, as in hepadnaviruses, the pregenomic 35S RNA (pgRNA) is first encapsidated and subsequently reverse transcribed within the virion (36). However, encapsidation of DNA following reverse transcription remains a possible alternative (24). The mechanism by which the terminally redundant RNA is encapsidated in hepadnaviruses and retroviruses has been widely studied. In retroviruses, the pgRNA is first specifically recognized by the Gag protein and then encapsidated (47), while in hepadnaviruses reverse transcription and encapsidation start after the recognition of the pgRNA by the N-terminal part of the reverse transcriptase (5). The specificity of encapsidation is determined by both the RNA and the viral protein involved.
In plant pararetroviruses, the 5' end of the pgRNA contains a long leader sequence with the potential to form a large stem-loop structure (14, 38). In CaMV, the formation of such an elongated hairpin structure (Fig. 1B) has been confirmed in vitro (22). A purine-rich sequence at the top of this hairpin is conserved in some caulimoviruses including CaMV, figwort mosaic virus (FMV), and carnation etched ring virus, and in badnaviruses such as rice tungro bacilliform virus, sugar cane bacilliform virus, and dioscorea alata bacilliform virus (21, 38). In CaMV, deletion of this sequence drastically retarded the occurrence of symptoms in infected plants but did not influence the transient expression of a reporter gene downstream of the mutated leader in host plant protoplasts (14). The function of this sequence is not known, but it has been proposed to act as a packaging signal or to be involved in dimerization of pgRNA (14, 21). Experiments performed in vitro, however, argue against the involvement of the purine-rich sequence in the dimerization process of the CaMV pgRNA leader (22).
Retroviral Gag polyproteins are cleaved by the viral protease into the matrix, capsid, and nucleocapsid proteins, which rearrange and assemble during maturation to form infectious particles (35). The zinc finger domains in the nucleocapsid of retroviruses are critical for viral replication and participate directly in genome recognition and encapsidation (1, 6, 12, 20, 34, 45). One of the best-studied examples is human immunodeficiency virus 1 (HIV-1) (18), for which the three-dimensional structure of the nucleocapsid bound to RNA stem-loop 3 of the HIV-1 leader has been determined (11).
The CaMV coat precursor protein is processed by the viral aspartic proteinase (49). After processing, derivatives carrying the central domain (p44, p39, and p37) are found as coat proteins associated with the virion, while the acidic N- and C-terminal portions have not been detected (27, 33). Each of the major coat proteins (CP) contains a basic region flanking a zinc finger motif (C-X2-C-X4-H-X4-C) that is conserved among retroelements (10). A synthetic peptide covering this region binds zinc ions (26). In FMV, the zinc finger is essential for virus viability (44).
The characteristics shared by the coat protein of CaMV and the Gag protein of retroviruses suggest the possibility that these viruses use similar mechanisms to encapsidate their pregenomic and genomic RNAs, respectively. In the present study, using the yeast three-hybrid system (46), we have found a specific interaction between the coat protein of CaMV and the conserved purine-rich sequence in the central part of the CaMV pgRNA leader. As in retroviruses, the zinc finger domain of the CaMV CP is critical for both interaction with CaMV pgRNA and viral infectivity.
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MATERIALS AND METHODS |
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The components of the three-hybrid system, including the controls used in our experiment, were kindly provided by Marvin Wickens, University of Wisconsin (46).
Hybrid RNAs. Two annealed complementary oligonucleotides covering bases 268 to 355 of the CaMV 35S RNA leader (Strasbourg strain) (17) were cloned into the SmaI site of pIII/MS2-2 (46). Sense and antisense orientation clones are called LS and LAS, respectively. The iron response element (IRE) RNA was cloned in the same position by SenGupta et al. (46). RNA secondary-structure analysis was performed using the MFOLD program (Wisconsin package version 6.0; Genetics Computers Group, Madison, Wis.) at 25°C.
Hybrid proteins. Hybrid protein 1 (see Fig. 2A), containing the DNA binding domain (LexA) and the RNA binding domain of the MS2 coat protein, is integrated into the genome of the yeast strain L40-coat. To obtain hybrid protein 2, the full-length open reading frame IV (ORF IV) (pIV) and its variants (CPs, numbered with the amino acid positions at which they start and end) were cloned in frame with the GAL4 activation domain in plasmid pGAD 424 (Clontech) (4). The NcoI-SalI pIV fragment from plasmid p(1-489) (31) was cloned directly into NcoI- and SalI-restricted pGAD 424. CP77-454 and CP77-411 were described previously (24). CP77-489 was obtained by replacing the BanII-BamHI fragment of CP77-454 with the BanII-BamHI fragment of pIV. CP225-454, CP272-454, CP315-454, CP347-454, CP391-454, and CP402-454 were amplified by PCR with the 5'-end oligonucleotides 5'-gcgatgtacaccgaattcttaggac-3', 5'-gaaaagaacgaattcaagacagaactgg-3', 5'-cagtttagaattcgcggcaaagatagtc-3', 5'-gtgttgtgaattcggagaagcttcaacag-3', 5'-ccgatcaggaaaagaattcaagccc-3', and 5'-gctcaaagcaagaattctgcccaaaaggcaag-3', respectively, and the 3'-end oligonucleotide 5'-gaatgaatagatcttgaactccttcatagg-3'. The PCR fragments were cut in EcoRI and BglII sites present at their 5' and 3' ends, respectively, and cloned into the corresponding sites in pGAD 424. All clones were derived from the Strasbourg strain of CaMV. The zinc finger mutations were introduced in the context of CP272-454 by using PCR-mediated site-directed mutagenesis.
CP315-489 was also amplified by PCR with the same 5'-end oligonucleotide used for CP315-454 and the 3'-end oligonucleotide 5'-acgttcggatcctgctcagtctgagtctgag-3'. The PCR fragment was cut with EcoRI and BamHI and cloned into EcoRI and BglII sites in pGAD 424. The cloning of ORF III into pGAD 424 is described in reference (30). ORF V was amplified by PCR with the 5'-end oligonucleotide 5'-gaacccggggatcctgatggatcatctacttctgaagact-3' and the 3'-end oligonucleotide 5'-tgaactgcagtagatctcggatttcaattaggaattaacct-3'. The product was cloned BamHI-blunt into plasmid pBluescript BamHI-SmaI and then cut with XhoI and filled in with the DNA polymerase I large (Klenow) fragment. Thereafter, it was cut with BamHI and cloned into pGAD 424. The vector pGAD 424 was cut with SalI, filled in with the DNA polymerase I Klenow fragment, and then cut with BamHI. ORF VII was amplified by PCR with the 5'-end oligonucleotide 5'-tggtgaattcgccatgaatcggtttaag-3' and the 3'-end oligonucleotide 5'-gtactgtcgacaggatcctttattgttccagaa-3' followed by digestion with EcoRI-BamHI and cloned into pGAD 424 digested with the same enzymes. To obtain the ORF VI clone, the XmaI-PstI fragment from pGBTTAV (24) was cloned directly into XmaI-PstI-restricted pGAD 424.Yeast culture. L40-coat strain (46) was grown in synthetic dropout (SD) minimal medium without tryptophan. Following transformation using the lithium acetate method (19), positive transformants were selected on SD medium lacking tryptophan and leucine and/or uracil. The transformants were allowed to grow at 30°C for 3 to 4 days.
-Galactosidase filter assay.
A total of 20 colonies were
restreaked on fresh plates and were allowed to grow for a further 2 days. They were then transferred to a nitrocellulose filter, frozen in
liquid nitrogen, thawed, and assayed for the appearance of blue color
by using 5-bromo-4-chloro-3-indolyl-
-D-galactoside (X-Gal) as the substrate of
-galactosidase, as described previously (43), and incubated at 30°C.
-Galactosidase liquid assay.
Five different transformants
were grown in minimal medium for 18 h to obtain an aliquot that
was diluted in fresh medium to give an optical density of approximately
0.25. The aliquots were allowed to grow for 3 h to obtain an
optical density of between 0.5 and 0.8, frozen in liquid nitrogen, and
thawed four times for lysis. The yeast lysates were assayed for
-galactosidase enzymatic activity (43) using ONPG
(o-nitrophenyl-
-D-galactopyranoside) (Fluka).
The enzymatic activity was determined in five independent transformants
and in at least three independent experiments. One unit of
-galactosidase was defined as the amount which hydrolyzes 1 µmol
of ONPG to o-nitrophenol and D-galactose per min
per cell (37).
Mutations of the zinc finger in the virus. Following cloning of the HpaI-SmaI fragment of pCa540 (which contains the genome of the CM4-181 CaMV strain) (13, 39) into plasmid pTZ 19R, mutations were introduced using site-directed mutagenesis. The mutants obtained were recloned into the pCa540 context by exchanging MluI-XmaI fragments and were analyzed by DNA sequencing. The infection was carried out using a procedure described previously (13, 39).
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RESULTS |
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CaMV CP interacts with the central part of the pgRNA leader.
The yeast three-hybrid system (46) is a genetic method to
detect and analyze RNA-protein interactions, whereby the binding of a
bifunctional RNA to each of two hybrid proteins activates the
transcription of a reporter gene in vivo (Fig.
2A). We used this system to test whether
there is a specific interaction between any of the CaMV proteins and
the conserved purine-rich sequence from the central region of the CaMV
pgRNA (35S RNA) leader (nucleotides 268 to 355 [Fig. 1B and 2B]). The
schematic representation of the fused transcript expressed from vector
pIII/MS2-2 is represented in Fig. 2C. This hybrid RNA was called leader
sense (LS). The same sequence in antisense orientation (LAS), the MS2
RNA alone, and an RNA containing the IRE (29) were also
tested.
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-galactosidase gene as seen by filter assay only for the viral coat
protein construct. In this positive case, the colonies turned blue
after 1 h.
To confirm that this interaction was due to the bridge formed by the
hybrid RNA between MS2 CP and CaMV CP, several control plasmids were
used, i.e., plasmids that code for the hybrid RNA alone, the GAL4
activation domain alone, or the fusion between the GAL4 activation
domain and the coat. No signal was obtained in any of these cases
(results not shown). Although colonies expressing the GAL4-CP77-454
fusion and either MS2, IRE, or LAS RNA turned blue in the
-galactosidase filter assay after prolonged incubation (5 or 6 h), the rapid appearance of the blue color (1 to 2 h) with the
GAL4-CP77-454 protein and the LS RNA indicated a specific interaction.
Relative
-galactosidase activities resulting from the interaction
between CP and the different RNAs are shown in Fig. 2D. The interaction
between CP and the LS RNA is about five times stronger than that
obtained with either the MS2 RNA alone or the MS2 RNA fused to the IRE
or LAS, indicating that CP interacts preferentially with the central
part of the leader sequence.
Both the zinc finger and the basic domain of CP are important for
the specific interaction with the leader.
To map the region of the
CaMV CP responsible for the specific interaction with the LS RNA, a
series of N- and C-terminal deletion mutants (Fig.
3A) were introduced in frame with the
GAL4 activation domain (hybrid protein 2 [Fig. 2A]) into the pGAD 424 vector (see Materials and Methods). All the constructs were transfected
alone or together with the plasmid expressing the LS RNA in the yeast strain L40-coat. Colonies containing either the plasmids expressing CaMV CP or the plasmid expressing the LS RNA alone did not turn blue
after more than 6 h when analyzed using the
-galactosidase filter assay (results not shown). When both plasmids were present, colonies turned blue in 1 to 2 h (Fig. 3A, right side). The
interaction was lost when the zinc finger motif was removed
(CP77-411). CP391-454 and CP402-454 do contain the zinc finger
motif, but the basic domain is drastically shortened. This might
indicate that the basic region is also important for the interaction.
The constructs pIV and CP77-489, as well as the very short constructs
CP391-454 and CP402-454, did not show the blue color. In a previous
analysis, full-size pIV and CP77-489 also failed to show any
interaction with the ORF VI-encoded protein (pVI) in the two-hybrid
system, although the truncated construct CP77-454 did so. The reason
in both cases might be either that the C-terminal acidic domain
destabilizes the protein (10) or that it masks the
interaction domain. An additional construct, CP315-489 (Fig. 3A),
which differs from the positively interacting CP315-454 only by
inclusion of the C-terminal acidic domain, was confirmed by Western
blot analysis to be stably expressed in yeast (results not shown).
Since CP315-489 did not interact with the LS-RNA, masking of the
interacting domain appears likely.
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-galactosidase liquid
assay. The activity of the
-galactosidase is shown relative to the
interaction between the CP77-454 protein and the LS RNA (Fig. 3B). As
shown above, the interaction of CP77-454 with the LS RNA is specific
compared to that the MS2 and the LAS RNAs. The same was true for
CP225-454, CP272-454, and CP315-454 when the interaction with the LS
RNA was compared to that obtained with the LAS RNA. The strength of the
interaction of CP272-454 and CP315-454 with the LS RNA was
drastically reduced although still specific compared with LAS RNA. The
specificity of the interaction was lost when the basic domain was
partially deleted, as shown by the interaction between CP347-454 and
the LS and LAS RNAs, respectively.
Our results indicate that the zinc finger domain of the CP and part of
the basic domain are required for the interaction with the LS RNA. The
shortest protein capable of a specific interaction was CP315-454,
which contains, in addition to the complete basic domain, part of a
putative
-helix (amino acids 330 to 346) that might be involved in
protein-protein interaction (9).
Mutations in the zinc finger of the CaMV capsid protein abolish
both virus infectivity and interaction with the leader.
To see
whether the zinc finger motif of CaMV CP is important for the
infectivity of this virus, we mutated some of the most important
conserved amino acids, i.e., cysteine and histidine residues forming
the zinc ion complexes, and additionally, aromatic amino acids
considered important for the specificity of zinc finger interaction
(10) (Fig. 4). Turnip
(Brassica rapa) plants were inoculated mechanically with
wild-type and mutated viruses (Ca583, Ca584, Ca586, Ca587, and Ca588).
Symptoms appeared after 3 weeks on plants inoculated with wild-type
virus. In contrast, even after 2 months, no symptoms appeared on plants
inoculated with any of the mutant viruses.
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-galactosidase filter assay. No
blue color appeared in any colony corresponding to the zinc finger
mutants (Fig. 4).
These results indicated that the zinc finger motif-mutated amino acids,
including aromatics and the ones responsible for the interaction with
zinc ions (cysteines and histidine), are crucial for virus infectivity
and are also important for the interaction with the LS RNA in the
three-hybrid system.
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DISCUSSION |
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Several reports have described the interaction between CaMV CP and nucleic acids (7, 9, 15, 24, 48) but none have described the specific interaction between CP and RNA that is believed to be responsible for the encapsidation of the pgRNA. To study this, we selected the purine-rich sequence in the middle part of the leader because of its conservation in most caulimoviruses and badnaviruses. Our approach was to use an in vivo method, the yeast three-hybrid system (46), that permits the analysis of protein-RNA interactions. We confirm that CP (CP77-454) interacts with RNA in general. However, the interaction is much stronger with the central part of the CaMV pgRNA leader (LS) than with other RNAs such as LAS, MS2 RNA, or IRE RNA. Similar results had been reported for the HIV-1 Gag protein, which interacts more strongly with the HIV-1 RNA viral encapsidation signal than with the IRE RNA or the encapsidation signal of either Moloney or Harvey murine sarcoma virus (2).
The zinc finger motif of the nucleocapsid protein is very important for infectivity in retroviruses. There are several studies showing that deletion or point mutation of the very highly conserved amino acids in this domain result in noninfectious viruses (see reference 47 for a review). Also, it has been previously shown for another pararetrovirus, FMV, that mutation of all the cysteines and the histidine of the zinc finger abolishes the infectivity of the virus (44). Here, we confirm this observation for CaMV CP. In addition, some of the zinc finger mutants were tested in the three-hybrid system, and none of them interacted with the central part of the leader. However, the zinc finger of CaMV CP alone is not sufficient for the specific interaction. The minimal protein CP315-454, which still interacts specifically with the LS RNA, contains the zinc finger, the basic domain, and a preceding region forming a putative helix containing two cysteines conserved in plant pararetroviruses. This region has been suggested to be important for the CP-CP interaction (9).
Our findings indicate that the interaction between the CP and the central part of the leader might play a role in the encapsidation of the CaMV pgRNA, similar to that in retroviruses. On the other hand, the encapsidation mechanism of CaMV might share some characteristics with the encapsidation mechanism of hepadnaviruses, since, as in hepadnaviruses but not in retroviruses, the reverse transcriptase of CaMV is expressed separately from CP (8), implying a mechanism to target it to the capsid (5, 41).
The central part of the CaMV RNA leader, which we found to interact specifically with the CaMV capsid protein, is not present in the 19S subgenomic RNA. However, it is still present in spliced forms of CaMV RNA (28). How could the spliced RNA be excluded from the packaging process? One possibility is that the leader structure of the spliced RNA is melted and occupied by scanning ribosomes while that of the unspliced RNA is not. Preservation of the central part of the unspliced leader structure is possible due to the shunt mechanism of translation initiation (16, 42), which excludes this region from the scanning process and hence from melting (23). Another possibility is that for successful packaging, not only the central part of the CaMV RNA leader but also other parts, e.g., the primer binding site, which is absent from spliced RNA, are required. Such a requirement might guarantee that the reverse transcriptase is included in the packaging and assembly process. Furthermore, RNA dimerization might be a prerequisite for efficient packaging (3) and the corresponding dimerization signal might be located within the intron.
Both terminal regions of the precoat protein (pIV) are very acidic and are removed during maturation. The N-terminal acidic region was implicated in inactivating the nuclear targeting signal, such that only CPs lacking this region are transported to the nucleus (31). Interestingly, the full-length pIV capsid preprotein and also other versions of this protein, CP77-489 and CP315-489, which are N-terminally truncated but contain the complete C-terminal sequence, did not interact with LS RNA in the three-hybrid system (Fig. 3A). CP315-489 does not contain the destabilizing N-terminal domain (A. Karsies, D. Leclerc, and T. Hohn, unpublished data), suggesting that the interaction of the coat protein with RNA is masked by the acidic C-terminal domain. Thus, the C terminus of pIV might have regulatory functions, e.g., preventing the binding of RNA and thereby guaranteeing its availability as mRNA until enough viral proteins (including the protease) are produced.
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ACKNOWLEDGMENTS |
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We thank Helen Rothnie, Dave Kirk, Witold Filipowicz, Mikhail Pooggin, Helena Morales, and Johannes Fütterer for the critical reading of the manuscript; Yvan Chapdelaine, Denis Leclerc, and Etienne Herzog for supplying some of the clones and for helpful discussion; and Mike Rothnie for the help with pictures.
We thank the "Eidgenössische Stipendienkomission für Ausländische Studierende" for supporting Orlene Guerra-Peraza.
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FOOTNOTES |
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* Corresponding author. Mailing address: Friedrich Miescher-Institut, Maulbeerstrasse 66, 4058 Basel, Switzerland. Phone: (061) 6976672. Fax: (061) 6973976. E-mail: hohn{at}fmi.ch.
Permanent address: Centro de Bioplanta, Ciego de Avila, Cuba.
Present address: IPCB-UMR 7519, 67084 Strasbourg, France.
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