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Journal of Virology, October 2005, p. 13166-13172, Vol. 79, No. 20
0022-538X/05/$08.00+0 doi:10.1128/JVI.79.20.13166-13172.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Alain Kohl,
Jane C. Osborne,
Angela McLees, and
Richard M. Elliott*
Division of Virology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G11 5JR, Scotland, United Kingdom
Received 12 May 2005/ Accepted 19 July 2005
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The bunyavirus genome consists of three segments of single-stranded RNA of negative, or ambisense, polarity. The largest segment (L) codes for an RNA-dependent RNA polymerase (L protein), the medium segment (M) codes for the two glycoproteins (Gn and Gc), and the smallest segment (S) encodes the nucleoprotein N. Viruses of some genera also encode nonstructural proteins either on the M (called NSm) or the S segment (called NSs). Viral replication takes place in the cytoplasm, while budding generally occurs at the Golgi apparatus (3, 26). As in other negative-stranded viruses, the RNA genome serves as the template for the synthesis of mRNAs and full-length, positive-sense antigenomic RNAs that in turn are templates for synthesis of progeny negative-stranded genomes. Reverse genetic systems developed for BUNV (7), La Crosse (4), Rift Valley fever (16, 22), Toscana (1), Uukuniemi (12), Crimean-Congo hemorrhagic fever (11), and Hantaan (10) viruses have shown that transcription and replication of artificial minigenomes require only two viral proteins, the polymerase L and N proteins.
The primary function of the N protein is the encapsidation of genome and antigenome RNAs to form a biologically active structure, the viral ribonucleoprotein or RNP. The RNPs have a "panhandle" structure in which the 3' and 5' genome termini are able to base pair (21). For BUNV, N was shown to bind specifically to the 5' terminus of the S genome segment, suggesting cotranscriptional encapsidation (24) of nascent viral RNA.
Bunyavirus N proteins vary in size from 25 to 30 kDa (orthobunya-, phlebo-, and tospoviruses) to 50 kDa (hanta- and nairoviruses), with little homology detected between the N proteins of viruses in different genera. A homotypic N-protein interaction implicated in the nucleocapsid structure has been extensively studied for the viruses of the Hantavirus genus; the N protein forms stable trimers (2, 18) that seem to bind specifically the panhandle structure of the RNA (23). The interaction sites on N proteins of several hantaviruses have been mapped and were shown to be principally in the N-terminal and C-terminal domains (see reference 20). Here we analyzed the homotypic interaction of the 26-kDa N protein of BUNV, the prototype virus of the Orthobunyavirus genus, using yeast and mammalian two-hybrid systems, coimmunoprecipitation, and chemical cross-linking experiments.
BUNV N-protein homotypic interaction detected in yeast and mammalian two-hybrid systems. BUNV N-N interaction was tested using a commercial yeast two-hybrid system, Matchmaker 3, obtained from Clontech (Palo Alto, CA). The full-length N open reading frame (ORF) was amplified by PCR using pTM1-BUNN (9) as the template and was cloned into EcoRI/PstI-digested binding domain (BD)-containing plasmid pGBKT7 (pBD) or EcoRI/XhoI-digested activation domain (AD)-containing plasmid pGADT7 (pAD) to produce pBD-BUNN or pAD-BUNN, respectively. Saccharomyces cerevisiae AH109 strain (17) was cotransformed using the lithium acetate method (14). Yeast cotransformed with the plasmid of interest and the other respective empty vector (pBD or pAD) was used as a negative control. Further controls for protein-protein interaction provided in the Matchmaker 3 system included pGADT7-T and pGBKT7-53 (positive controls) and pGADT7-T and pGBKT7-Lam (negative controls).
Yeast growth was observed only in the case of pAD-BUNN and pBD-BUNN cotransformants and the pGADT7-T plus pGBKT7-53 positive control (Fig. 1A, sectors a and c). No growth was observed when one N construct was cotransformed with the other empty vector or with the pGADT7-T plus pGBKT7-Lam negative control (Fig. 1A, sectors b, d, and e). These results show that N can homodimerize in the yeast two-hybrid system.
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FIG. 1. Bunyamwera virus N-N interaction in the yeast and mammalian two-hybrid systems. (A) N-N interaction in the yeast two-hybrid system using the Matchmaker 3 system (Clontech). S. cerevisiae strain AH109 was cotransformed with plasmids as indicated, and clones were selected on minimal synthetic dropout (SD) medium lacking leucine and tryptophan (SD-L-W), as these two markers are used for maintenance of the plasmids in the cells. Cotransformant clones were then transferred onto SD medium lacking leucine, tryptophan, histidine, and adenine (SD-L-W-H-A) in the presence of 5 mM 3-amino-1,2,4 triazol (3-AT) (Sigma-Aldrich) to test for protein-protein interaction. 3-AT is a natural inhibitor of the yeast HIS3 protein and was used to prevent low levels of HIS3 expression, thus suppressing background growth on SD medium without histidine. (B) N-N interaction in the mammalian two-hybrid system. HeLa cells were transfected with the CAT reporter plasmid pG5CAT, which contains GAL4 binding sites, and 1 µg of each plasmid as follows: positive-control plasmid pM3VP16, which encodes both the DNA-binding and transactivation domains as one fusion protein (lane 1); positive-control plasmids pVPMxA and pGalMxA (lane 2); pSGN and pVPBUNN (lane 3); pSGN and pAASN (lane 4); pSGN only (lane 5); pVPBUNN only (lane 6); and pAASN only (lane 7). CAT activity was assayed in cell extracts 48 h posttransfection as described previously (6, 15).
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Transiently expressed N protein multimerizes. To extend the above results, we studied N-N interaction during transient expression in mammalian cells. The plasmid pBD-BUNN contains a T7 RNA polymerase promoter sequence downstream of the BD, allowing expression of a mRNA encoding a c-Myc-tagged version of the N protein. To assess the capacity of the c-Myc-tagged N protein to form nucleocapsid structures, we used the previously described BUNV minireplicon system (31). BSR-T7/5 cells, which stably express T7 RNA polymerase (5), were cotransfected with pTM1-BUNL, pTM1-FF-Luc, the minigenome pT7riboBUNMRen(), and increasing amounts of the N-encoding plasmid pBD-BUNN or pT7riboBUNN. The pT7riboBUNN plasmid was chosen as the positive control for this test, as it produces mRNA encoding native N protein under control of the T7 RNA polymerase promoter. The c-Myc-tagged N protein was functional in the minireplicon system (Fig. 2A) though it was less active than the native N protein: when 1 µg of each N-expressing plasmid was transfected, the tagged N resulted in 14-fold-less luciferase signal. This result indicated that the tagged N protein was able to encapsidate minireplicon RNA and multimerize to form a functional RNP; therefore, we used it in coimmunoprecipitation experiments.
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FIG. 2. c-Myc-tagged N protein is functional. (A) Activity of the c-Myc-tagged N protein in the minireplicon assay. Approximately 5 x 105 BSR-T7/5 cells were transfected with 0.25 µg pTM1-BUNL, 0.1 µg pTM1-FF-Luc, 0.3 µg pT7riboBUNMRen() (all plasmids described in reference 31), and the indicated amount of the N-expressing plasmid, using 5 µg DAC-30 (Eurogentech) per transfection. Transfection efficiencies were normalized by measuring luciferase expression from cotransfected pTM1-FF-Luc. (B) Coimmunoprecipitation of c-Myc-tagged and native N proteins. Approximately 5 x 105 vTF7-3-infected CV-1 cells were transfected with 2.5 µg of pBD-BUNN and pTM1-BUNN (lane 1), pBD-BUNN and pTM1 (lane 2), pBD and pTM1-BUNN (lane 3), and pBD and pTM1 (lane 4) using 5 µg DAC-30 per transfection. At 16 h posttransfection, cells were labeled for 3 h with 50 µCi [35S]methionine, and immunoprecipitations were performed overnight at 4°C using anti-c-Myc monoclonal antibody 9E10 (9). Radiolabeled proteins were separated on a 12% polyacrylamide gel. (C) Coimmunoprecipitation of native N and c-Myc-tagged N in the presence (+) or absence () of RNase A treatment. Cell extracts were treated with 5 µg/ml (final concentration) RNase A for 30 min at 37°C before immunoprecipitation and gel electrophoresis.
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To study the possibility of a higher degree of N multimerization, suggested by the coimmunoprecipitation experiment, transiently expressed wild-type N protein was cross-linked with 1 mM dithiobis(succinimidylpropionate) (DSP) (Pierce), a homobifunctional and reduction-sensitive cross-linking agent. Transfected cells were treated with DSP as recommended by the manufacturer, and cell extracts were separated on a denaturing polyacrylamide gel followed by Western blotting using an anti-N polyclonal antibody (Fig. 3A). A ladder of proteins with molecular masses corresponding to those of N multimers (50 kDa, 75 kDa, 100 kDa, etc.) (Fig. 3A, lane 1) was detected in the absence of reducing agent. When ß-mercaptoethanol was added to the loading buffer, the cross-linking agent was reduced, and a single band corresponding to N monomers was observed (Fig. 3A, lane 3). This experiment was repeated with RNase A treatment of the extract with a concentration of 10 µg/ml prior to cross-linking, but no difference was observed (Fig. 3B). The authenticity of N-protein multimerization was confirmed by the appearance of a similar pattern of N-protein bands following cross-linking of BUNV-infected cell extract (Fig. 3C).
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FIG. 3. Cross-linking of Bunyamwera virus N protein. (A) Cross-linking of transiently expressed N. CV-1 cells were infected with vTF7-3 and transfected with 2.5 µg of pTM1-BUNN (lanes 1 and 3) or with empty pTM1 plasmid as a control (lanes 2 and 4), and at 16 h posttransfection cells were cross-linked using 1 mM DSP. Cross-linked samples were separated on a 12% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in the presence (+) or absence () of ß-mercaptoethanol (ß-me) in the loading buffer, and proteins were detected by Western blotting with anti-N antibodies as described previously (31). (B) Effect of RNase A treatment. CV-1 cells were infected with vTF7-3 and transfected with 2.5 µg of pTM1-BUNN (lanes 1 and 3) or empty pTM1 plasmid as a control (lanes 2 and 4). Cells were scraped in phosphate-buffered saline (PBS) and freeze-thawed three times, and the RNase A was added to the final concentration of 10 µg/ml. The samples were cross-linked by direct addition of DSP to 1 mM final concentration. Analysis by SDS-PAGE, without ß-mercaptoethanol in the loading buffer, and detection of N protein were performed as described above. (C) Cross-linking of N protein in virus-infected cells. CV-1 cells were infected with BUNV at a multiplicity of infection of 10 (+) or mock infected (). At 16 h postinfection, cell extracts were cross-linked using PBS containing 1 mM DSP. Analysis by SDS-PAGE, without ß-mercaptoethanol in the loading buffer, and detection of N protein were performed as described above.
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FIG. 4. Functional analysis of N-terminal deletion mutants of N protein. (A) Schematic representation of the N mutants. The numbers are amino acid positions. (B) Activities of N11-233 and Ndel11-20 mutants in the minireplicon assay. BSR-T7/5 cells were transfected with 0.25 µg pTM1-BUNL, 0.3 µg pT7riboBUNMRen(), 0.1 µg pTM1-FF-Luc, and 0.1 µg of pTM1-BUNN (pTM1), pTM1-BUNN11-233 (N11-233), or pTM1-BUNNdel11-20 (NdeI11-20) as indicated. After incubation overnight, cells were lysed and luciferase activities were measured in a dual reporter assay (Promega). Transfection efficiencies were normalized by measuring firefly luciferase expression from pTM1-FF-Luc. The amount of N protein expressed was analyzed by Western blotting (WB) using an anti-N antibody (anti BUN N) in the blot at the bottom of the panel. (C) Cross-linking of Bunyamwera virus N11-233 protein. CV-1 cells were infected with vTF7-3 and transfected with 2.5 µg of pTM1-BUNN (lane 1), empty pTM1 (lane 2), or pTM1-BUNN11-233 (lane 3). Cell extracts were cross-linked using PBS containing 1 mM DSP. Cross-linked samples were analyzed by Western blotting with an anti-N antibody.
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The C-terminal 17 amino acids of the orthobunyavirus N proteins also show a high degree of conservation (8). We investigated the importance of this region in N multimerization by generating a C-terminally truncated construct of the N protein lacking amino acids 217 to 233. A double mutant, lacking amino acids 1 to 10 and 217 to 233 was also generated by PCR. Both products were cloned into the restriction sites BsmBI/PstI of pTM1, producing pTM1-BUNN1-216 and pTM1-BUN11-216, respectively (Fig. 5A). Both mutants were tested for activity in the minireplicon system (Fig. 5B), and neither showed activity compared to the native N protein. Both mutant proteins had slightly decreased stability, and the amount of mutant N-encoding plasmid was adjusted empirically to ensure a level of expression similar to that of the native N-protein positive control. To investigate the loss of activity, the multimerization capacity of both mutants was assessed by cross-linking (Fig. 5C). The N1-216 mutant was able to form dimers and small amounts of trimers but was severely impaired in its ability to form higher multimers. In contrast, the double mutant was not able to form any oligomers, suggesting that the deleted sequences are essential for N multimerization. Thus, we have identified sequences involved in both binding sites of the interaction. The homodimerization observed for both the N-terminal and C-terminal single deletion mutants suggests that BUNV N can form head-to-head and tail-to-tail types of interaction.
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FIG. 5. Functional analysis of C-terminal deletion and double mutants of N protein. (A) Schematic representation of the N mutants. The numbers are amino acid positions. (B) Activities of N1-216 and N11-216 mutants in the minireplicon assay. BSR-T7/5 cells were transfected with 0.25 µg pTM1-BUNL, 0.3 µg pT7riboBUNMRen(), 0.1 µg pTM1-FF-Luc, and 0.1 µg pTM1-BUNN (pTM1), 0.2 µg pTM1-BUNN1-216 (N1-216), or 1 µg pTM1-BUNN11-216 (N11-216) as indicated. After incubation overnight, cells were lysed and luciferase activities were measured in a dual reporter assay (Promega). Transfection efficiencies were normalized to firefly luciferase activity. The amount of N protein expressed was analyzed by Western blotting (WB) using an anti-N antibody (anti BUN N) in the blot at the bottom of the panel. (C) Cross-linking of Bunyamwera virus N1-216 and N11-216 proteins. CV-1 cells were infected with vTF7-3 and transfected with 2.5 µg of pTM1-BUNN (lane 1), empty pTM1 (lane 2), pTM1-BUNN1-216 (lane 3), or pTM1-BUNN11-216 (lane 4). Cell extracts were cross-linked using phosphate-buffered saline containing 1 mM DSP. Cross-linked samples were analyzed by Western blotting with an anti-N antibody.
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The presence of substantial amounts of tetramers in the cross-linking experiment (Fig. 3) indicates that the oligomerization strategy of BUNV N protein differs from the model proposed for hantavirus N multimerization. The BUNV nucleocapsid protein seems to form multimers by addition of one N molecule at a time and not by association of preformed trimers (19). Our results are thus in agreement with those obtained with tomato spotted wilt tospovirus N protein (29), where the interaction of N in solution was shown to be a continuous process, leading to the formation of multimers, including tetramers; interaction was shown to involve amino acids 1 to 39 and 233 to 248 of the 258-residue-long tospovirus N protein. The apparent conservation of the multimerization mechanism of the N proteins of orthobunyaviruses and tospoviruses, coupled with previous sequence comparisons of the viral polymerase ORFs that demonstrated the orthobunyavirus L protein was more homologous to the tospovirus L than to the hantavirus or phlebovirus polymerase proteins (25), indicate closer evolutionary similarity of these two groups of animal- and plant-infecting bunyaviruses.
J.C.O. received a CASE studentship from BBSRC and Roche Products Ltd. Research in R.M.E.'s laboratory is funded by the Wellcome Trust.
Present address: Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905. ![]()
Present address: Centre for Emergency Preparedness and Response, Health Protection Agency, Porton Down, Salisbury SP4 0JG, United Kingdom. ![]()
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