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Journal of Virology, January 2003, p. 696-700, Vol. 77, No. 1
0022-538X/03/$08.00+0 DOI: 10.1128/JVI.77.1.696-700.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Contribution of the Zinc Finger to Zinc and DNA Binding by a Suppressor of Posttranscriptional Gene Silencing
Rene van Wezel,1 Huanting Liu,2 Zirong Wu,3 John Stanley,4 and Yiguo Hong1*
Horticulture Research International, East Malling, West Malling, Kent ME19 6BJ,1
Centre for Biomolecular Science, University of St. Andrews, Fife KY16 9ST,2
Department of Disease and Stress Biology, John Innes Centre, Colney, Norwich NR4 7UH, United Kingdom,4
Department of Biology, East China Normal University, Shanghai 200062, China3
Received 18 July 2002/
Accepted 1 October 2002

ABSTRACT
The zinc finger C
36-X1-C
38-X7-C
46-X6-H
53 of the nuclearly localized
C2 protein of
Tomato yellow leaf curl virus China is involved
in pathogenicity and suppression of posttranscriptional gene
silencing (PTGS). Here, we demonstrate that the zinc finger
is indispensable for the C2 protein to bind zinc and DNA. Mutation
of cysteine residue C
36, C
38, or C
46 reduced the zinc and DNA
binding capacity of C2 protein. When expressed from potato virus
X, all three mutants, C2-C
36R, C2-C
38N, and C2-C
46I, tagged
with a green fluorescent protein (GFP) were still capable of
transporting GFP into but aggregated abnormally in nuclei. Our
data establish that zinc- and DNA-binding activity correlates
with C2-mediated pathogenesis and PTGS suppression.

TEXT
Posttranscriptional gene silencing (PTGS) in plants, RNA interference
in animals, and gene quelling in fungi share a common molecular
mechanism in which a target RNA is transinactivated by homology-dependent
RNA degradation, representing a conserved cellular defense system
for controlling foreign gene expression across kingdoms (
3,
8,
14,
31,
39,
42). In plants, PTGS protects the host against
virus infection, down-regulates transgene expression, and may
also be an important component in the control of development
(
39,
42). Consistent with the active role of PTGS in antiviral
defense, plant viruses have evolved counterattack functions
by encoding proteins that are capable of suppressing PTGS. PTGS
suppressors often enhance viral pathogenicity, and a number
of them have been characterized, including 2b, HC-Pro, P1, and
P19 proteins from cucumoviruses, potyviruses, sobemoviruses,
and tombusviruses; p25 movement protein of
Potato virus X (PVX);
and AC2 and C2 proteins of
African cassava mosaic virus and
Tomato yellow leaf curl virus China (TYLCV-C) (
6,
37,
39). There
is much variation in the extent of PTGS suppression by different
virus-encoded suppressors that may be mediated by targeting
distinct steps in the PTGS pathway (
2,
40,
41).
Geminiviruses are a family of unique small circular single-stranded (ss) DNA viruses that replicate via double-stranded (ds) DNA intermediates by a rolling circle mechanism in plant cell nuclei (15). TYLCV-C, a distinct species of the genus Begomovirus in the family Geminiviridae, has a monopartite genome resembling the DNA A component of bipartite begomoviruses (43). We have previously demonstrated that TYLCV-C C2, a nuclearly localized protein, induces necrosis and suppresses PTGS when expressed from a PVX vector and that a cysteine-rich motif (C36-X1-C38-X7-C46-X6-H53) is required for C2 protein-mediated pathogenesis and PTGS suppression (37, 38). However, whether the C2 protein binds zinc and indeed whether the cysteine-rich domain represents an authentic zinc-finger motif remained unclear.
To address these issues, we first used the Bac-to-Bac system (Invitrogen Life Technologies) to express wild-type and mutant C2 proteins, all of which have a six-histidine affinity tag. Baculovirus containing the C2 gene or its derivatives was recovered after homologous recombination between the baculovirus expression vector pBac/C2, pBac/C2-C36R, pBac/C2-C38N, or pBac/C2-C46I (Table 1) and the viral DNA according to the manufacturer's protocol. Sf9 cells were then infected with recombinant baculoviruses, and after 72 h of incubation at 28°C, Sf9 cells were harvested, resuspended in extraction buffer (EB; 50 mM Tris-HCl [pH 8.0], 1 mM phenylmethylsulfonyl fluoride) containing 50 mM NaCl, and lysed by sonication. Insoluble pellets were discarded after centrifugation, and high-speed clarified supernatants were collected. Aliquots of Sf9 extracts were adjusted to either 50, 100, or 200 mM NaCl. The amount of C2 protein in Sf9 extracts was normalized using competitive enzyme-linked immunosorbent assay (19) and an antihistidine monoclonal antibody (Amersham Pharmacia Biotech).
We performed a zinc-affinity pull-down assay, for which extracts
from wild-type or recombinant baculovirus-infected Sf9 cells
containing equal amounts of wild-type or mutant C2 protein in
either 50, 100, or 200 mM NaCl were incubated with 50-µl
aliquots of zinc chelate affinity resins (iminodiacetic acid-Sepharose
6B; Sigma) preequilibrated with EB containing either 50, 100,
or 200 mM NaCl, as appropriate. Resins were then washed three
times with the same buffer, resuspended in 100 µl of 1
x gel loading buffer (
21), and boiled for 3 min before loading
samples onto a sodium dodecyl sulfate-15% polyacrylamide gel.
After electrophoresis, proteins were immobilized on nitrocellulose
membranes, immunodetected with the ECL detection system by use
of a monoclonal antibody raised against the histidine tag (Amersham
Pharmacia Biotech), and analyzed using a PhosphorImager. In
a low-salt (50 mM NaCl) buffer, C2 protein and all three mutants
remained bound to the resin. There was little difference in
binding affinity between the wild-type protein and mutant C2-C
46I
at this salt concentration, although mutants C2-C
36R and C2-C
38N
bound less well (Fig.
1A). A reduction in the ability of all
three mutants to bind to the resin in comparison with the wild-type
protein became more evident at 100 mM NaCl and was particularly
marked for mutants C2-C
36R and C2-C
38N (Fig.
1B). Some wild-type
protein remained bound at 200 mM NaCl, although none of the
three mutants was capable of binding at this salt concentration
(Fig.
1C). Our data indicate that histidine tags made little
contribution to the differential capabilities of the wild-type
and mutant C2 proteins to bind zinc. Indeed, the affinity of
the wild-type and mutant proteins for zinc chelate resin indicates
that C2 protein is capable of binding zinc, as reported for
Tomato golden mosaic virus TrAP (transcriptional activator protein;
also known as AL2 or AC2) (
16), and that the cysteine-rich C
36-X1-C
38-X7-C
46-X6-H
53 domain represents a bona fide zinc finger required for this
purpose. We previously demonstrated that mutation of C
36, C
38,
and C
46 eliminated C2 protein-mediated induction of necrosis
and PTGS suppression (
37) and that these mutations also significantly
reduce the ability of C2 protein to bind zinc, suggesting that
the three cysteines are additionally responsible for this activity.
Interestingly, mutation of C
38N and C
36R had a greater adverse
effect on zinc binding activity than mutation of C
46I.
Zinc-finger proteins frequently possess DNA-binding activity.
We therefore investigated whether C2 protein bound ssDNA and/or
dsDNA and the role of the zinc finger in DNA binding. To achieve
this,
Escherichia coli strain BL21 (DE3; Invitrogen Life Technologies)
was transformed with pEHT/C2, pEHT/C2-C
36R, pEHT/C2-C
38N, or
pEHT/C2-C
46I (Table
1), and expression of C2, C2-C
36R, C2-C
38N,
and C2-C
46I was induced with 0.4 mM IPTG (isopropyl-ß-
D-thiogalactopyranoside)
and analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.
Viral and nonviral ssDNA and dsDNA fragments were
32P labeled
using a Ready-to-Go labeling kit (Amersham Pharmacia Biotech),
and Southwestern assays were performed to determine interactions
between C2 protein and ssDNA and dsDNA probes with equal amounts
of radioactivity as described by Liu et al. (
24). The C2 protein
bound to TYLCV-C
C2 gene ssDNA (405 nucleotides) and dsDNA (405
bp) probes (Fig.
2A and C). At 300 mM KCl, all three mutants
bound to ssDNA and dsDNA, although C2-C
46I bound less efficiently
to ssDNA at this salt concentration. At 600 mM KCl, C2 protein
bound dsDNA more efficiently than ssDNA (Fig.
2B and D). At
this salt concentration, however, all three mutants failed to
bind ssDNA, and the ability of C2-C
38N and C2-C
46I to bind dsDNA
was significantly reduced in comparison with the wild-type protein.
Moreover, in a parallel experiment, the C2 protein was found
to preferably bind dsDNA probes (1,161 bp) prepared from a TYLCV-C
unrelated plant gene, the
LFY-like gene involved in flower development
(
23; H. Liu and Y. Hong, unpublished data). The results indicate
that C2 protein binds DNA in a sequence-nonspecific manner with
a preference for dsDNA, in contrast to other TrAPs that bound
ssDNA with higher efficiency (
16,
27), and that the cysteine-rich
motif participates in this binding activity. Although C2 protein
is basic, its interaction with DNA is not necessarily due to
a net positive charge since the basic protein lysozyme (pI,

9.6) bound neither ssDNA nor dsDNA under the prevailing conditions.
Clearly, DNA binding by C2 protein was affected by mutation
of the three zinc-finger cysteine residues. C2-C
36R, C2-C
38N
and C2-C
46I mutants were unable to bind ssDNA in high salt (600
mM KCl), and both C2-C
38N and C2-C
36R were significantly impaired
in their ability to bind dsDNA under these conditions, although
C2-C
46I maintained substantial binding activity, reflecting
the effect of these mutations on zinc binding.
To better understand the relevance of the observed biochemical
properties to C2 protein function, the cellular localization
of mutants C2-C
36R, C2-C
38N, and C2-C
46I was investigated. PVX
RNA transcripts were produced by in vitro transcription and
mechanically inoculated onto
Nicotiana benthamiana plants as
previously described (
7). Leaf tissues infected with PVX/C2-GFP
(C2), PVX/C2-C
36R-GFP (C2-C
36R), PVX/C2-C
38N-GFP (C2-C
38N),
and PVX/C2-C
46I-GFP (C2-C
46I) were collected 7 days postinoculation,
cut into 3-mm-wide strips, vacuum infiltrated, and fixed overnight
in 4% paraformaldehyde-100 mM phosphate buffer (pH 7.0). Tissues
were then infiltrated with 15% sucrose-100 mM phosphate buffer
(pH 7.0), embedded in 5% low-melting-point agarose, and sectioned
in a cryostat at -20°C (OTS; Bright Instruments). Ten-micrometer
sections were mounted in 50% glycerol containing 1 µg
of DAPI (4',6'-diamidino-2-phenylindole)/ml and examined using
a Zeiss Axiophot equipped with a Nikon Digital Camera Coolpix995.
When expressed as green fluorescent protein (GFP)-tagged fusion
proteins from PVX vectors (PVX/C2-C
36R-GFP, PVX/C2-C
38N-GFP,
and PVX/C2-C
46I-GFP), all three mutants localized to the nucleus
(Fig.
3, top panels), resembling the behavior of the wild-type
protein fused to GFP expressed from PVX/C2-GFP (
38). However,
fluorescence associated with the mutants was irregularly scattered
in the nuclei of leaf mesophyll cells and was distinct from
the even distribution of C2-GFP fluorescence. DAPI staining
indicated that the nuclei remained intact (Fig.
3, bottom panels),
and no nuclear structural alterations were observed by transmission
electron microscopy (R. Van Wezel and Y. Hong, unpublished data),
suggesting that the zinc-finger mutants aggregate abnormally
in nuclei. This remarkable effect may not be due simply to alteration
of the primary structure of the protein. Indeed, several C2
protein mutants such as C2-K
17D, C2-HR
21DV, and C2-KK
25DI containing
different amino acid substitutions were capable of transporting
GFP into nuclei, and the nuclearly localized GFP fluorescence
was evenly distributed (R. van Wezel, X. Dong, H. Liu, P. Tien,
J. Stanley, and Y. Hong, Abstr. XII Int. Congr. Virol., p. 148,
2002).
The three cysteine residues of the zinc finger were changed
to either arginine, asparagine, or isoleucine. The choice of
mutations was based on the notion that the physicochemical properties
of these amino acids are largely unrelated to that of cysteine
as discussed previously (
37). Thus, the effect of mutations
on biological and biochemical functions of the C2 protein would
become detectable. Another important issue is that such amino
acid replacements should impose a minimum effect on the C2 protein
structures. As revealed by Chou-Fasman prediction (
9), the wild-type
C2 protein and mutant C2-C
38N possessed essentially the same
secondary structures. Mutant C2-C
46I formed a secondary structure
similar to that of wild-type C2 and mutant C2-C
38N proteins,
with the exception of having a ß-sheet around the
zinc finger instead of an

-helix. C2-C
36R had a slight different
overall conformation but without local structural alterations
in the region of the zinc finger. Surprisingly, C2-mediated
zinc- and DNA-binding activities were mostly affected by the
mutation of C
38N, while the C
36R mutation had the least effect
on C2 binding to DNA and the C2-C
46I mutation had stronger zinc-binding
activity than the other two mutants (Fig.
1 and
2). Therefore,
the specificity of effects observed in this report is unlikely
due to the mutant amino acids globally interfering with C2 folding
or conformational stability, which would simultaneously impair
all of its activities. Indeed, the modified proteins are soluble
in plant cells and at least partially functional since they
are still transported to the nucleus. It is likely that the
zinc finger specially affects the tertiary and/or quaternary
structure of the C2 protein. Single substitution of the three
cysteine residues with any amino acid may lead to the formation
of unusual disulfide bonds between the two SH groups of the
remaining nonmutated cysteine residues of the zinc finger within
or between C2 protein molecules. Another possibility is that
the zinc finger could control the ability of the C2 protein
to form stable structural complexes as has been described for
other zinc- and DNA-binding proteins (
22). As a consequence
of such structural changes, the C2 protein altered its biochemical
activities in zinc and DNA binding and its cellular biological
property, which led to the deficit of its biological functions
in pathogenesis and PTGS suppression in planta.
In summary, we have found that a correlation exists between the biochemical properties of the C2 protein encoded by the monopartite begomovirus TYLCV-C and its biological functions in pathogenesis and PTGS suppression. In plants, PTGS represents an effective defense mechanism against infection caused by RNA and DNA viruses. Initiation, propagation of a systemic silencing signal, and maintenance have been recently proposed to be the three components in the process of PTGS (28, 29) which can be targeted by PTGS suppressors. Notably, potyviral HC-Pro affects a step coincident with, or upstream of, the production of small RNAs that is necessary for PTGS maintenance (25, 26). In contrast, the PVX p25 cell-to-cell movement protein and the 2b protein of Cucumber mosaic virus appear to prevent silencing signal spread (12, 40). While most suppressors that have been identified are from RNA viruses and are involved in virus movement, TrAP and C2 proteins are encoded by ssDNA begomoviruses (1, 4, 20, 37, 41). Collectively, TrAP and its C2 protein homologue, encoded by bipartite and monopartite begomoviruses, respectively, specifically modulate viral gene expression at the transcriptional level, enhance plant susceptibility to viral infection, contribute to viral pathogenicity, and suppress PTGS (5, 10, 11, 13, 16-18, 32-36, 37, 41). TrAP exhibits sequence-nonspecific DNA binding activity and is confined to the nucleus (16, 27, 30, 32, 38). TrAP has also been reported to be phosphorylated and to bind zinc (16). However, the relevance of these diverse molecular and cellular properties of TrAP to pathogenesis and PTGS suppression is less well understood.
Although TrAP and C2 proteins participate in the control of specific viral genes and are probably also involved in host gene expression, these proteins are not canonical transcriptional activators due to their sequence-nonspecific interaction with DNA. It is believed that the zinc- and ssDNA-binding activity is not particularly relevant to TrAP-mediated transcriptional regulation (16, 27), and this may also be the case for the TYLCV-C C2 protein. Clearly, this raises the question of the biological significance of the observed zinc- and DNA-binding activity to the infection process. The results of this study and a previous mutagenesis analysis (37) have indicated that the altered biochemical behavior of the three zinc-finger mutants in zinc and DNA binding correlates with a loss of biological function in inducing necrosis and suppressing PTGS in planta. This suggests that zinc and DNA binding play either a direct or indirect role in C2 protein-mediated pathogenesis and PTG5 suppression.

ACKNOWLEDGMENTS
We thank D. Baulcombe for providing the original PVX-based vector
and are grateful to T. M. A. Wilson for his encouragement throughout
this work.
This project was supported in part by the Biotechnology and Biological Sciences Research Council.

FOOTNOTES
* Corresponding author. Mailing address: Horticulture Research International, East Malling, West Malling, Kent ME19 6BJ, United Kingdom. Phone: 44 173 284 3833. Fax: 44 173 284 9067. E-mail:
yiguo.hong{at}hri.ac.uk.


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Journal of Virology, January 2003, p. 696-700, Vol. 77, No. 1
0022-538X/03/$08.00+0 DOI: 10.1128/JVI.77.1.696-700.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.