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Journal of Virology, June 2003, p. 7078-7092, Vol. 77, No. 12
0022-538X/03/$08.00+0     DOI: 10.1128/JVI.77.12.7078-7092.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Basic Residues of the Helix Six Domain of Influenza Virus M1 Involved in Nuclear Translocation of M1 Can Be Replaced by PTAP and YPDL Late Assembly Domain Motifs

Eric Ka-Wai Hui, Subrata Barman, Tae Yong Yang, and Debi P. Nayak*

Department of Microbiology, Immunology and Molecular Genetics, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, UCLA School of Medicine, Los Angeles, California 90095-1747

Received 9 January 2003/ Accepted 25 March 2003


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ABSTRACT
 
Influenza type A virus matrix (M1) protein possesses multiple functional motifs in the helix 6 (H6) domain (amino acids 91 to 105), including nuclear localization signal (NLS) (101-RKLKR-105) involved in translocating M1 from the cytoplasm into the nucleus. To determine the role of the NLS motif in the influenza virus life cycle, we mutated these and the neighboring sequences by site-directed mutagenesis, and influenza virus mutants were generated by reverse genetics. Our results show that infectious viruses were rescued by reverse genetics from all single alanine mutations of amino acids in the H6 domain and the neighboring region except in three positions (K104A and R105A within the NLS motif and E106A in loop 6 outside the NLS motif). Among the rescued mutant viruses, R101A and R105K exhibited reduced growth and small-plaque morphology, and all other mutant viruses showed the wild-type phenotype. On the other hand, three single mutations (K104A, K105A, and E106A) and three double mutations (R101A/K102A, K104A/K105A, and K102A/R105A) failed to generate infectious virus. Deletion ({Delta}YRKL) or mutation (4A) of YRKL also abolished generation of infectious virus. However, replacement of the YRKL motif with PTAP or YPDL as well as insertion of PTAP after 4A mutation yielded infectious viruses with the wild-type phenotype. Furthermore, mutant M1 proteins (R101A/K102A, {Delta}YRKL, 4A, PTAP, 4A+PTAP, and YPDL) when expressed alone from cloned cDNAs were only cytoplasmic, whereas the wild-type M1 expressed alone was both nuclear and cytoplasmic as expected. These results show that the nuclear translocation function provided by the positively charged residues within the NLS motif does not play a critical role in influenza virus replication. Furthermore, these sequences of H6 domain can be replaced by late (L) domain motifs and therefore may provide a function similar to that of the L domains of other negative-strand RNA and retroviruses.


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INTRODUCTION
 
Influenza virus matrix protein (M1) is a relatively small, highly conserved protein (252 amino acids [aa] in type A and 248 aa in type B viruses). M1 is the most abundant protein in virus particle and plays critical roles in many aspects of virus replication. These include (i) dissociation of M1 from the M1/viral ribonucleoprotein (vRNP) complex during the entry and uncoating of infecting virus, (ii) nuclear entry of M1, (iii) interaction of M1 with vRNP to form M1/vRNP complex, (iv) role of M1 in the exit of vRNP from the nucleus into the cytoplasm, (v) interaction of M1 with viral envelope proteins (hemagglutinin [HA], neuraminidase, and ion channel M2), (vi) membrane binding of M1, (vii) dimer/oligomer formation of M1, (viii) role of M1 in virus budding, including recruitment of viral components at the assembly site and recruitment of host components for budding and release of virus particles (reviewed in references 29, 40, and 41).

The M1 monomer is 60 Å long (55), possessing two globular regions (aa 1 to 164 and 165 to 252) linked by a protease-sensitive loop. The structure mostly consists of helix and loops and is devoid of ß strand (60). The N-terminal fragment (aa 1 to 164) has been crystallized in both acidic and neutral pH, and the three-dimensional structure has been determined by X-ray diffraction analysis (3, 20, 59). This fragment contains eight loops (L) and nine helices (H), but the next loop (aa 159 to 164) was not resolved in X-ray diffraction (3, 20, 21, 59). The helix 6 (H6) domain (aa 91 to 105) of M1 provides multiple functional domains including nuclear localization signal (NLS), RNA/RNP binding, and transcription inhibition motifs.

Four basic residues in 101-RKLKR-105 were shown to function as the NLS for the nuclear entry of M1 (45, 69, 72). However, the role of NLS sequence in M1 in virus biology remains unknown. M1 lacking the NLS sequence remains in the cytoplasm when expressed alone but enters the nucleus when expressed with vRNP (45). It has been shown that M1 interacts with vRNP and inhibits transcription (65, 70, 71). Furthermore, M1 has been shown to bind single-stranded RNA nonspecifically in vitro (12, 27) and to bind to vRNP in virus-infected cells (35, 50, 56) and in virus particles (2, 7, 58) but not to nucleoprotein (NP) expressed alone (23, 74). It was therefore postulated that M1 binds to vRNP via negative charges of the exposed RNA in vRNP. Clusters of positive charges on the H6 (aa 91 to 105) are believed to interact with negative (PO4-) charges of RNA. However, this view has been questioned by a number of workers, since the C-terminal fragment (aa 165 to 254) which does not bind to RNA can bind to vRNP and the N-terminal fragment (aa 1 to 164) which binds RNA does not bind vRNP (5, 6, 45). Furthermore, only the entire M1 (aa 1 to 252) which binds both RNA and vRNP causes transcription inhibition (6). It therefore becomes important to define the role of positive charges on the H6 of M1.

M1 is the major driving force of the influenza virus budding, since in the absence of M1 virus-like particles (VLPs) are not formed (16, 30) and M1 is believed to be the key component in recruiting and assembling viral components required for budding at the plasma membrane (reviewed in references 29, 40, and 41). In addition, the matrix proteins of many negative-strand viruses and retroviruses have been shown to possess specific motifs called L (late) domains, which are involved in recruiting the host components required for budding and release of virus particles (reviewed in references 9, 14, 36, and 46). So far, three different motifs in viral matrix proteins have been shown to function as the L domain. These are PPP(P)Y (PY motif or proline-rich motif), P(T/S)AP(P), and YXXL motifs, found in matrix proteins of negative-strand viruses as well as in retroviruses, including human immunodeficiency virus. These motifs have been shown to interact with a number of cellular proteins (reviewed in references 9, 14, 36, and 46). However, no such L domain has yet been identified for influenza viruses.

To define functional significance of the NLS and neighboring sequences of M1 in influenza virus biology, we have mutated the amino acid sequences in this region and studied their effect on virus rescue by reverse genetics and on virus replication. We observed that mutation of specific sequences of the NLS motif and the neighboring region can have a profound effect in virus rescue and growth. Furthermore, we observed that the nuclear translocation function of the NLS sequence of M1 is not required for virus rescue or growth in MDCK cells and that the YRKL sequence of influenza virus M1 can be effectively replaced by PTAP or YPDL, suggesting that YRKL and the neighboring region may function as the L domain in influenza virus replication.


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MATERIALS AND METHODS
 
Cell lines and viruses. Madin-Darby canine kidney (MDCK) cells were maintained in Dulbecco's modified Eagle medium (DMEM) (Invitrogen, Rockville, Md.) supplemented with 10% heat-inactivated fetal bovine serum (Atlanta Biologicals, Norcross, Ga.) and antibiotics (100 U of penicillin-G/ml and 100 µg of streptomycin/ml). 293T cells were maintained in Opti-MEM (Invitrogen) supplemented with 5% fetal bovine serum and antibiotics. Influenza virus strain A/WSN/33 (H1N1) was used in these experiments, and the stock viruses were prepared by infecting MDCK cells at a multiplicity of infection (MOI) of 0.001 and incubating them at 33°C in virus growth medium (VGM) (minimum essential medium supplemented with 0.2% bovine serum albumin [BSA], 4% basal medium Eagle vitamin, 10 mM HEPES [pH 7.2], 0.155% NaHCO3, 0.0015% DEAE-dextran, 100-U/ml penicillin-G, 100-µg/ml streptomycin).

Generation of transfectant viruses using reverse genetics and preparation of mutant stock viruses. The WSN M gene in the Pol I-Pol II plasmid (22) was used as a template for site-directed mutagenesis. Mutagenesis reactions were performed by using a QuickChange site-directed mutagenesis kit (Stratagene, La Jolla, Calif.). Primers used in these reactions will be provided upon request. Transfectant viruses were generated using a procedure modified from one reported earlier (22). All eight Pol I-Pol II plasmids containing influenza virus genes were kindly provided by Robert Webster, St. Jude Research Hospital, Memphis, Tenn. Briefly, eight plasmids (1 µg each; seven Pol I-Pol II constructs of wild-type [WT] HA, neuraminidase, NP, NS, PA, PB1, PB2, and one Pol I-Pol II construct of either WT or mutated M gene) were mixed with transfection reagent (2 µl of TransIT LT-1 [Panvera, Madison, Wis.] per microgram of DNA), incubated at room temperature for 45 min, mixed with Opti-MEM in a final volume of 1 ml, added to 293T cells (106 cells in a 35-mm dish), and incubated at 37°C. Eight hours later, the DNA-transfection mixture was replaced with VGM. Twenty-two hours later, transfected cells were shifted to 33°C and incubated for 16 h. Then, TPCK (L-1-tosylamide-2-phenylethyl chloromethyl ketone)-treated trypsin (Sigma, St. Louis, Mo.) (final concentration, 0.5 µg/ml) was added and incubated further for 32 h, at which time the supernatants were collected and titers of infectious virus were determined by plaque assay. We routinely got 107 PFU/ml directly from the supernatant after DNA transfection. Individual plaques were isolated, resuspended in virus dilution buffer (phosphate-buffered saline plus [PBS+] [137 mM NaCl, 4.2 mM Na2HPO4, 2.7 mM KCl, 1.5 mM KH2PO4, 0.5 mM MgCl2, and 1 mM CaCl2] supplemented with 0.2% BSA, 0.005% DEAE-dextran, 100 U of penicillin-G/ml, and 100 µg of streptomycin/ml), and inoculated into MDCK cells at a MOI of 0.001 (1.2 x 107 cells in a 25-cm2 flask for 100% confluence). Infected cells were incubated in VGM with trypsin (0.5 µg/ml), and the supernatants were harvested at 48 h postinfection (p.i.), subjected to plaque assay for titer determination, and used as virus stocks.

Plaque assay. For determining the numbers of PFU, MDCK cell monolayers (1.5 x 106 cells in a 35-mm dish for 100% confluence) were washed with PBS+. Stock virus was diluted for the appropriate input MOI in virus dilution buffer, layered on the MDCK monolayers, and incubated for 1 h at 37°C. Unabsorbed viruses were removed by washing with VGM, and cell monolayers were overlaid with agar overlay medium (VGM supplemented with 0.6% low-melting-point agarose [Invitrogen]) and incubated at 33°C. For determining temperature sensitivity (ts), plaque assays were performed at 33°C (the permissive temperature) or 37 or 39.5°C (nonpermissive temperature). After 3 days' incubation at the permissive temperature or nonpermissive temperature, the agar overlay was removed and the MDCK cell monolayer was washed with PBS and stained with 0.1% crystal violet (in 20% ethanol) for 1 min. Visible plaques were counted, and numbers of PFU/ml were determined. The plaque numbers and sizes were obtained from at least three separate experiments, each using triplicate culture plates. All data are expressed as mean (standard deviations were less than 10%) for three to four independent experiments. The significance of the difference (P) between values was compared using Student's t test, and P values of <0.001 were considered significant.

Labeling and immunoprecipitation of M1 mutant proteins. At 18 h posttransfection, 293T cells were starved in Met- and Cys-free (Met-/Cys-) DMEM (Invitrogen) for 30 min and then pulse labeled with 100 µCi of 35S-protein label (ICN Biomedicals Inc., Irvine, Calif.) for 2 h. For pulse-chase experiments, labeled cells were incubated with Opit-MEM I containing excess (0.1 mM) cold Met and Cys for 3 h. Cells were then lysed in 1 ml RIPA buffer (50 mM Tris-HCl [pH 7.5], 150 mM NaCl, 1% Triton X-100 [TX-100], 0.5% sodium deoxycholate, 0.1% sodium dodecyl sulfate [SDS], 1x proteinase inhibitor cocktail), immunoprecipitated with anti-M1 antibody (Biodesign International, Saco, Maine), and analyzed by SDS-12% polyacrylamide gel electrophoresis (PAGE).

Analysis of the protein composition of virus particles. Infected MDCK cells were labeled from 4 to 16 h p.i. with 250 µCi of 35S-protein label using nine parts Met-/Cys- DMEM and 1 part DMEM and containing 0.2% BSA. At 16 h p.i., the medium was harvested and clarified by low-speed centrifugation, and virions were pelleted by ultra-centrifugation (150,000 x g) through a 25% sucrose cushion. Pelleted virions were resuspended with TNE buffer (10 mM Tris [pH 7.4], 100 mM NaCl, 1 mM EDTA) by overnight shaking at 4°C and lysed in RIPA buffer with 1% SDS at 37°C for 90 min. The lysate was either analyzed directly or immunoprecipitated in 1 ml of RIPA buffer (0.1% SDS) by antibodies against M1, NP, or HA and analyzed by SDS-PAGE.

Indirect immunofluorescence. MDCK cells (4 x 105) were grown on tissue culture chamber slides (Nunc, Naperville, Ill.), and 293T cells were grown on BD BioCoat poly-D-lysine-laminin culture slides (BD Biosciences, Bedford, Mass.). Cells were infected with WT or mutant virus (MOI of 3), and at 5 h p.i. and 13 h p.i., infected cells were washed with PBS+ and fixed in 100% acetone for 10 min at -20°C. After three washes with PBS (5 min each), fixed cells were incubated with goat anti-M1 antibodies (diluted 1:30 in PBS containing 3% BSA) for 1 h at room temperature. Cells were then washed three times for 15 min each in PBS and incubated with fluorescein isiothiocyanate-conjugated anti-goat Immunoglobulin G (Santa Cruz Biotechnology Inc., Santa Cruz, Calif.) diluted 1:120 in PBS containing 3% BSA for 35 min at room temperature and washed again four times with PBS (15 min each) and once with water (1 min) and blown dry. Cells were then mounted in 50% glycerol in PBS (pH 9). The slides were viewed under an Axioskop 2 fluorescence microscope (Carl Zeiss, Thornwood, N.Y.).

Thin-section electron microscopy. Thin-section electron microscopy of virus-infected cells was carried out as described previously (4). Briefly, MDCK cells were grown on a 3.0-µm-pore-size polycarbonate filter (Corning Incorporated, Corning, N.Y.) for 60 h and infected at a MOI of 3 on the Transwell (25, 26). At 10 h p.i., virus-infected cells were cross-linked in 2% glutaraldehyde (EM-grade) in PBS+ and postfixed with 1% osmium tetroxide in PBS+. Filters were dehydrated, cut out from filter units, and embedded in Epon. Sections (60 nm) were stained with uranyl acetate and lead citrate and then examined with a JEOL JEM-100CX electron microscope (JEOL Ltd., Tokyo, Japan).


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RESULTS
 
Mutational analysis of the NLS and the neighboring region in the H6 domain. H6 domain of M1 is exposed outside and contains multiple overlapping functional domains (Fig. 1A). Deletion and substitution analyses have implied that positively charged residues in the H6 region (101-RKLKR-105; Fig. 1B) provide the NLS function for translocating M1 protein into the nucleus (69, 72). Two other positively charged residues, Lys95 and Lys98, are also present in the neighboring region, forming a continuous positive surface on the H6 domain of the M1 structure (Fig. 1B and C). In order to investigate the function of the H6 domain in influenza virus M1 protein on virus replication, we initially made individual alanine substitution of amino acids in the H6 region encompassing Lys95 to Asp106 (Fig. 2A). Alanine substitution has been extensively used in defining functional domains of proteins, since alanine substitution removes any perturbing effect of side chains and maintains the conformation flexibility of the structure (reviewed in reference 38). cDNA transfection and immunoprecipitation analysis showed that all of the M1 mutants were expressed to similar levels in transfected 293T cells (Fig. 2B). We then used an eight-plasmid Pol I-Pol II transfection system in 293T cells for rescuing infectious influenza virus by reverse genetics (22). We observed that all single Ala mutants except three (K104A, R105A, and E106A) could be rescued into infectious virus. Of these three lethal mutants, two were in the NLS sequence (K104A and R105A) and one was in the neighboring L6 loop (E106A). Next, we used the rescued viruses to determine the effects of these alanine substitutions on a multiple cycle of virus growth and plaque morphology in MDCK cells in the presence of trypsin. We observed that all single-alanine mutants except one (R101A) exhibited the WT phenotype in virus growth and plaque morphology (Fig. 2C and D). The R101A mutant grew to a 100-fold-lower titer than the WT virus (Fig. 2C). Plaque size measurement at 3 days p.i. on MDCK cells overlaid with low-melting-point agarose containing trypsin (0.5 µg/ml) also showed that only the mutant R101A virus exhibited smaller plaques (Fig. 2D). These sets of experiments indicated that the positively charged residues Arg101, Lys104, and Arg105 in the NLS motif of the H6 domain of M1 were important for the influenza virus replication.



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  		FIG. 1. (A) Schematic diagram of influenza A virus M1 with functional domains. {alpha}-Helix 1 (H1) to helix 9 (H9) (black boxes) and intervening loops (L) are shown according to the work of Sha and Luo (59). The hydrophobic regions between aa 1 and 11, 62 and 68, and 114 and 133 are shown as lipid binding domains (LBD) (17, 18, 71), between aa 91 and 111 as RNA binding domain (65, 67), aa 90 and 110 and aa 129 and 164 as TID (45, 65, 69, 71), aa 101 and 105 as NLS (69, 72), and aa 148 and 162 as predicted CCHH zinc finger motif (Zn) (64). The interaction of M1 with NS2 or RNP is located within the C-terminal two-thirds (68, 71). The potential protein kinase C phosphorylation sites (circled P) are Ser70, Ser161, and Thr185 (51). (B) Amino acid sequence of the H6 domain (aa 91 to 105) and 106E. The positively charged amino acids are boxed in gray. Schematic diagram of the helix (H1 to H9) and loops. H6 is exposed on the surface (3, 20, 21, 59). The {alpha}-helical regions are indicated as cylinders, and the putative N and C termini are marked. (C) Helical wheel plot of H6 domain. Positively charged amino acids (gray shading) are exposed on the surface. (D) Amino acid sequence alignment of the H6 domains of M1 from different influenza A virus strains. The positively charged amino acids are boxed in gray. Variations are shown.



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  		FIG. 2. (A) Schematic representation of single-amino-acid mutations (aa 95 to 106). Amino acid sequence of the H6 domain (aa 95 to 105) and specific mutations are indicated. The positively charged amino acids are shown in gray. (B) Immunoprecipitation of M1 mutant proteins. At 18 h posttransfection, 293T cells were pulse labeled for 2 h. Cells were then lysed in RIPA buffer, immunoprecipitated with anti-M1 antibody, and resolved by SDS-12% PAGE. Autoradiographs from two separate gels are shown. (C) PFU titer of transfectant viruses. Transfected viruses were rescued by eight plasmids in transfection of 293T cells. MDCK cells were then infected with transfectant virus at a MOI of 0.001 and maintained in VGM containing 0.5 µg of trypsin/ml as described in Materials and Methods. Supernatants were collected at 48 h p.i. and assayed for numbers of PFU by plaque assay. Data represent mean values (n = 3). Asterisk, P < 0.001 (versus WT). (D) The plaque sizes for different mutant viruses on MDCK cells. Plaques were visualized at day 3, and diameters were measured. Data represent mean values (n = 4). Asterisk, P < 0.001 (versus WT).

To further determine if the positive charge of the basic residues exposed on the M1 surface or the specific amino acid residues were important for the function of this domain, we substituted each positively charged residue with another positively charged amino acid (i.e., K95R, K98R, R101K, K102R, K104R, and R105K) (Fig. 2A). In cDNA-transfected 293T cells, these mutant proteins exhibited similar levels of protein expression and stability (Fig. 2B), and infectious viruses were rescued from each of these mutants. Analysis of viral growth and plaque morphology showed that all of these mutants except the R105K mutant grew to a titer similar to WT virus growth and exhibited plaque morphology similar to that of the WT virus (Fig. 2C and D). The R105K mutant grew to a lower titer (100 times less) and produced significantly smaller plaques than other mutants or the WT virus (Fig. 2C and D). These results showed that in addition to the positive charge, Arg105 of the NLS in the H6 domain of the M1 protein provided some other important function in influenza virus replication, since it could not be fully replaced by Lys substitution.

To further analyze the function of these NLS and neighboring residues, we made a number of double Ala mutations (Y100A/L103A, R101A/K102A, R101K/K102R, K104A/R105A, and K102A/R105A) and a double substitution of positive charges (R101K/K102R) (Fig. 3A). Again all proteins were expressed in cDNA-transfected cells to the same level (Fig. 3B). Virus rescue experiments showed that mutations of Y100A/L103A and R101K/K102R yielded infectious virus with the WT phenotype. However, infectious virus could not be rescued after repeated attempts with any of the other three double mutants (R101A/K102A, K104A/R105A and K102A/R105A). Since these three double mutations included four basic residues of NLS, these positively charged residues provided some critical function in the influenza virus life cycle. Furthermore, lack of virus rescue from K104A/R105A mutation and reduced growth of the mutant R101A and R105K viruses (Fig. 2C) also supported the importance of these residues in virus replication.



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  		FIG. 3. (A) Schematic representation of the double-mutation constructs. (B) Immunoprecipitation and PAGE analysis of M1 mutant proteins. (C) Titer of transfectant viruses. (D) Plaque sizes for different mutants on MDCK cells. For details, see the legend to Fig. 2.

Characterization of R101A and R105K mutant viruses. Since R101A and R105K mutant viruses yielded a lower PFU titer and a smaller plaque size, we wanted to determine if the protein stability affected the function of these mutant proteins. Accordingly, 293T cells were transfected with mutant or WT M1 cDNAs, and protein expression and stability were determined by pulse and chase experiments. Results show that WT as well as mutant R101A and R105K proteins exhibited similar stability after chase (Fig. 4).



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  		FIG. 4. Stability of WT and R101A and R105K mutated M1 proteins. At 18 h posttransfection, 293T cells were pulse labeled for 2 h (lanes P) and then chased with excess Met and Cys for 3 h (lanes C). Cells were then lysed in RIPA buffer, immunoprecipitated with anti-M1 antibody, and analyzed by SDS-PAGE.

To determine if the R101A or R105K mutation caused any ts defect, the plaque size and plaque morphology in the absence or presence of trypsin were determined in MDCK cells at 33°C, 37°C, or 39.5°C at 3 days p.i. (Table 1). Results showed that although the development of plaque and the progression of plaque size were slower at 33°C than at 37 and 39.5°C, plaques produced by WT virus attained the same size by 3 days at all three temperatures. Both R101A and R105K mutants, on the other hand, produced smaller plaque sizes at all three temperatures. Thus, neither the R101A mutation nor the R105K mutation exhibited a significant ts defect.


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  		TABLE 1. Effect of temperature on virus growth and plaque morphologya

Since entry and exit of M1 from the cytoplasm to the nucleus and vice versa have been shown to be critical in the infectious cycle (52, 66), we determined the intracellular localization of mutant M1 proteins. Furthermore, since both Arg101 and Arg105 mutations are present in the NLS motif, we wanted to determine if these mutations affected nuclear localization of M1 in virus-infected cells. Accordingly, MDCK cells were infected with virus, fixed at 5 and 13 h p.i., and analyzed by indirect immunofluorescence (IF) by staining for M1 (Fig. 5). Members of our group and others (52, 66) have shown previously that in influenza virus-infected cells, M1 is predominantly nuclear early in the infectious cycle (5 h p.i.) but becomes cytoplasmic later (13 h p.i.) in the infectious cycle, indicating the exit of M1/vRNP complex from the nucleus into the cytoplasm. Infection of MDCK cells with all mutant viruses exhibiting the WT phenotype showed cytoplasmic and nuclear distribution of M1 similar to that for the WT virus at both 5 and 13 h p.i. (Fig. 5). R101A mutant virus also showed nuclear and cytoplasm distribution similar to that for the WT virus (Fig. 5A and B versus C and D). However, in R105K virus-infected cells, the mutant M1 protein exhibited a different intracellular distribution. The R105K protein appeared aggregated and was partially retained in the nucleus even at 13 h p.i. (Fig. 5E and F), suggesting that not only the positive charge but Arg105 itself provided some specific function which could not be replaced by Lys.




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  		FIG. 5. Intracellular distribution of M1 mutants by IF analysis of virus-infected MDCK cells. MDCK cells were grown on slides and infected with WT or mutant viruses at a MOI of 3.0. At 5 h p.i. (panels A, C, E, G, I, K, M, and O) or 13 h p.i. (panels B, D, F, H, J, L, N, and P), the cells were fixed and stained for M1 by IF with an anti-M1 antibody. (A and B) WT; (C and D) R101A; (E and F) R105K; (G and H) K102A; (I and J) K104R; (K and L) PTAP; (M and N) 4A+PTAP; (O and P) WT+PTAP. Representative fields from analysis of 20 fields of view in duplicate experiments are shown. Magnification, x558 (A-I) and 527 (I-P).

Since the M1 protein is a critical component in budding of virus particles, the mutant M1 protein can affect the budding process and alter the shape and size of virus particles (34, 54). We therefore examined the virus particles on the apical plasma membrane of infected MDCK cells by transmission electron microscopy. Accordingly, polarized MDCK cells grown on the polycarbonate filters were infected with WT, R101A, or R105K mutants at a MOI of 3. At 12 h p.i., infected cells were fixed for thin-section electron microscopy. Results (Fig. 6A) showed that the WT virus particles were mostly spherical and had a dense core. R105K mutant virus particles were also spherical and contained the dense cores as with the WT virus, but fewer particles were present on the cell surface (Fig. 6C). These results would support the IF data (Fig. 5F) that defective exit of M1/vRNP from the nucleus into the cytoplasm of R105K-infected cells would result in production of fewer virus particles. On the other hand, the mutant R101A virus-infected cells essentially contained the same number of virus particles on the cell surface as the WT virus-infected cells (Fig. 6B). However, many of these R101A mutant particles were elongated and filamentous in shape, and some were often empty and VLP-like, lacking vRNP cores. Some of the filamentous particles appeared to contain multiple spherical particles joined together (Fig. 6B).



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  		FIG. 6. Budding of virus particles by thin-section electron microscopy. MDCK cells grown on polycarbonate filter were infected with either WT, K101A, or K105R viruses at a MOI of 3.0. At 12 h p.i., infected cell monolayers on filters were cross-linked, postfixed, and embedded. Sixty-nanometer-thick sections were stained and examined. WT (A), R101A (B), and R105K (C). , normal virus particles; , empty VLPs; ->, elongated virus particles.

Since electron-microscopic analysis suggested that some R101A mutant virus particles were empty and therefore may contain less vRNP, we examined the viral protein composition by direct PAGE analysis of purified virions. Results (Fig. 7) showed that compared to the WT virus, the NP/M1 ratio was reduced to nearly half in R101A virions but remained essentially same in R105K virions. Similar results were obtained by immunoprecipitation of purified virion particles with specific antibodies against HA, NP, and M1 (data not shown). However, since spherical and filamentous particles were not separated in these experiments, the reduced NP/M1 ratio in R101A virus preparation could be due at least partly to an increased ratio of filamentous to spherical particles (54). Further studies are needed to define the cause of reduced infectivity and altered particle shape and size. These results suggest that R101A and R105K mutants produce less infectious virus by two different mechanisms. In R105K-infected cells, more M1 is retained in the nucleus and less is available in the cytoplasm. Consequently, these cells produce fewer virus particles. However, in R101A-infected cells, M1 normally exits from nucleus into the cytoplasm as in the WT virus-infected cells, but mutation affected bud formation and virus release. In addition, a defective vRNP-M1 interaction may also lead to production of more VLP-like noninfectious particles and fewer infectious particles.



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  		FIG. 7. Protein composition of purified WT, R101A, or R105K virion. Virus-infected MDCK cells were labeled from 4 to 16 h p.i. with 250 µCi of 35S-protein label. Supernatants were harvested and clarified, and labeled viruses in supernatants were pelleted through a 25% sucrose cushion by centrifugation. The pelleted particles were resuspended with TNE buffer, lysed in RIPA buffer with 1% SDS at 37°C for 90 min, and directly analyzed by SDS-12% PAGE. The position of viral proteins HA, NP, and M1 are indicated at the left of panel. The ratio based on HA, NP, or M1 is mentioned at the bottom of the gel. The data represent the average for three independent experiments with less than 10% variation.

Mutational analysis of YRKL sequence. Primary amino acid sequence of the H6 region showed that the NLS and adjacent sequence possesses 100-YRKL-103 sequence (Fig. 1B) and that this region is highly conserved among different influenza A strains (Fig. 1D). The YRKL motif is similar to the L domain motif (YXXL) found and implicated in budding of equine infectious anemia virus (EIAV) (43, 48, 49). We therefore wanted to define the functional significance of YRKL and neighboring sequence in influenza virus biology. Accordingly, we used single and multiple mutations, as well as deletion, substitutions, and insertions in this region. Initial analysis showed that single Ala (Y100A and L103A) (Fig. 2) or double Ala (Y100A/L103A) (Fig. 3) mutations did not affect either virus rescue or growth. In addition to single Ala mutation, we also made Y100F and Y100S (Fig. 2), where Tyr100 was replaced by a Ser residue, a nonconservative substitution that removes the aromatic ring while keeping a hydroxyl side chain. In Y100F, Tyr was replaced by Phe, where the aromatic ring was conserved. Infectious viruses could be rescued from both mutations, and both mutant viruses exhibited the WT phenotype, including virus growth and plaque morphology (Fig. 2). We then mutated Leu103 to L103I and L103V, since another tyrosine-based motif, such as YXX{Phi} ({Phi} = large hydrophobic residue, such as Ile or Val), found in the cytoplasmic tails of the varicella-zoster virus glycoprotein gE (42) and pseudorabies virus glycoprotein gE (62) and gB (13), has been implicated in internalization. Again, mutant viruses were rescued, and the rescued viruses exhibited the WT phenotype (Fig. 2). These data showed that neither the L103I mutation nor the L103V mutation had any effect on virus replication.

Next we replaced all four residues (100-YRKL-103) by Ala (4A) (Fig. 8A) and failed to rescue infectious virus from transfected 293T cells after repeated attempts (Fig. 8C). Immunoprecipitation analysis showed that that 4A mutant protein was expressed well in the transfected cells (Fig. 8B), suggesting that YKRL may provide some critical function in virus biology. This observation is also supported by the fact that the R101A/K102A double mutants also failed to generate infectious virus by reverse genetics (Fig. 3C). IF analysis of 293T cells transfected by R101A/K102A and 4A cDNAs showed that each mutant protein when expressed alone was present only in the cytoplasm (Fig. 9E and F), whereas the WT M1 protein was present in both the nucleus and the cytoplasm as expected (Fig. 9A). These results showed that 101-RK-102 was a part of the NLS involved in the nuclear translocation of M1 as reported previously (69, 72).



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  		FIG. 8. (A) Schematic representation of the YRKL mutation, deletion, replacement, or insertion constructs. Different L domain motifs were used for replacement or insertion. (B) Immunoprecipitation of M1 mutant proteins. (C) Virus titer of transfectant viruses. (D) Plaque sizes for different mutants on MDCK cells. For details, see the legend to Fig. 2.



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  		FIG.9. Intracellular distribution of M1 mutants by IF in cDNA-transfected 293T cells. 293T cells were transfected with WT or mutant M1 cDNA. At 8 h posttransfection, cells were fixed and stained for M1 by IF with an anti-M1 antibody. (A) WT; (B) K104A; (C) R105A; (D) Y100A/L103A; (E) R101A/K102A; (F) 4A; (G) {Delta}YRKL; (H) PTAP; (I) 4A+PTAP; (J) YPDL; (K) PPPY. Representative fields from analysis of 20 fields of view in duplicate experiments are shown. Magnification, x558.

Since the L domain of the EIAV Gag protein contains the YPDL (YXXL) motif (43, 48, 49), we wanted to see if the YPDL motif could replace YRKL in the influenza virus M1 protein. Therefore, we replaced YRKL with YPDL (Fig. 8A) and observed that the mutant protein was expressed efficiently (Fig. 8B). The mutant virus was rescued and exhibited a WT phenotype (Fig. 8C and D), showing that YPDL could functionally replace the YRKL motif of influenza virus M1. Many retroviruses and negative-stranded viruses contain PTAP as their L domain. To determine if PTAP could replace YRKL, we made the mutated cDNA containing PTAP (Fig. 8A) and attempted virus rescue by reverse genetics. Again, mutant virus containing the PTAP motif could be rescued and exhibited the WT phenotype (Fig. 8). It has been further shown that L domains in retroviruses can function at other positions in the Gag protein (1, 10, 43, 44, 67, 73). We therefore inserted PTAP after YRKL (WT+YRKL) and 4A substitution (4A+PTAP) (Fig. 8A). Again, both of these mutant proteins were expressed efficiently (Fig. 8B), and infectious viruses were rescued and exhibited the WT phenotype (Fig. 8C). Again, IF analysis of virus-infected cells showed that M1 entry and exit from the nucleus occurred normally as in WT virus-infected cells (Fig. 5K to P). However, when similar substitution was made with PPPY (Fig. 8A), another L domain motif, infectious virus could not be rescued after repeated attempts even though the mutant protein was expressed efficiently (Fig. 8B). IF analysis of cells transfected with mutant cDNAs (4A, PTAP, 4A+PTAP, YPDL, and PPPY) showed that these mutant proteins when expressed alone were all cytoplasmic, as expected due to the disruption of the NLS sequence. However, viruses with the WT phenotype can be rescued by reverse genetics from PTAP, 4A+PTAP, WT+PTAP, and YPDL mutant cDNAs (Fig. 8C and D), and entry and exit of these mutant M1 proteins were normal as in WT virus-infected cells (Fig. 5K to P). Taken together, these results suggest that the NLS function of 101-RKLKR-105 is not critical in influenza virus biology and that this region provides a function similar to that of the L domains of other viruses in virus budding and can be replaced by other L domains, such as YPDL and PTAP.


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DISCUSSION
 
The H6 domain of M1 possesses an {alpha}-helical structural conformation (Fig. 1B). Many nucleic acid binding proteins have been shown to provide the best nucleic acid-protein interaction when the protein adapts an {alpha}-helical conformation (61, 63). Therefore, it is of interest that positive charges of the NLS (aa 101 to 105), RNA binding domain (aa 90 to 105), and transcription inhibition domain (TID) are located within the {alpha}-helical conformation (Fig. 1A). NLS sequences often overlap the DNA- or RNA-binding domains in many nucleic acid binding proteins (28). A number of viral core-coat-matrix proteins also possess similar positively charged motifs (underlined) for multiple functions. These include Brome mosaic virus coat protein (CP), possessing the arginine-rich motif (7-KMTRAQRRAAARRNR-21) for interacting with viral genomic RNA and providing stability of the virion structure (8); cucumber mosaic virus CP N-terminal basic arm (11-RTSRRRRPRRGSR-23), providing functions for virion formation, infectivity, and cell-to-cell movement (57); Southern cowpea mosaic virus CP random domain arginine-rich region (22-RRKRRAKRR-30) for viral RNA interaction and virus assembly (32); and hepatitis B virus core protein C-terminal region (150-RRRGRSPRRRTPSPRRRRSQSPRRRRSQSR-179) for viral pregenomic RNA encapsidation and viral DNA maturation (24, 39).

By using cDNA transcription and expression, it has been shown that 101-RKLKR-105 provides the NLS function for nuclear translocation of the M1 protein (69, 72). Nuclear translocation of the M1 protein is a critical function required for interaction with vRNP and for exit of vRNP from the nucleus into the cytoplasm (reviewed in references 29, 41, and 47). However, nuclear translocation of M1 in virus-infected cells, unlike the case in cDNA-transfected cells, does not depend on the function of the NLS, since the mutant M1 protein lacking NLS can enter the nucleus when expressed with other viral proteins, particularly NP and vRNA (23, 45). These results, therefore, raise an important issue, whether nuclear translocation of M1 provided by the NLS motif is a critical functional requirement in the viral infectious cycle or whether the sequences in the NLS motif provide some other important functions in the virus life cycle. Recently, Liu and Ye (33) used single-amino-acid mutations and reverse genetics to analyze the functional significance of the NLS sequence (101-RKLKR-105) and concluded that these basic residues provide an important function in viral replication by translocation of M1 from the cytoplasm into the nucleus. For the present report we have made extensive mutational analysis of the NLS and the neighboring sequences and observed some similarity with and difference from their results. Our data show that all single-amino-acid mutations in this region except K104A and R105A yielded infectious virus. However, data by Liu and Ye (33) showed that K102N and R104N did not yield infectious virus. Thus, K102A was positive for virus rescue and viruses with the WT phenotype in our report, but K102N was negative in their report. On the other hand, R105A was negative in our work, but R105S was positive in their report. This difference is likely due to a combination of factors. (i) Virus rescue using transfection of eight separate plasmids may not always be 100%, in spite of optimized conditions and repeated attempts. This inefficiency becomes more pronounced for viruses such as the R105S mutant, which yielded a 100-fold-lower titer of virus (33). (ii) Alternatively, specific amino acid used in the R105A substitution versus the R105S substitution may be a critical factor. The role of specific amino acids is further supported by the fact that even the R105K mutation, which retained the positive charge, yielded 100-fold less infectious virus (Fig. 2C). As indicated earlier, the reduced virus yield with R105K is likely to due to more retention of the mutated M1 protein in the nuclei of infected cells (Fig. 5F). Both reports show that mutation of K104 was lethal for virus rescue and that mutation in R101 was tolerated but yielded 100-fold-lower titers of virus. As indicated in this report, the reduced virus yield with R101A and R105K was likely due to a different mechanism. Taken together, both reports show that the positive charged amino acids either individually or collectively play an important role in virus replication and growth.

However, since the NLS function overlaps with other functions, such as RNA/RNP binding, dimerization, and possible membrane binding by electrostatic interaction with positively charged residues, it is not clear if nuclear translocation of M1 provided by the NLS is a critical functional requirement for virus growth and replication. Furthermore, since M1 is a relatively small protein, the NLS sequence may facilitate, but may not be required in, nuclear entry of M1. However, NLS may aid in nuclear retention of M1 by interacting with vRNP or cellular proteins, such as histones (75). Furthermore, since M1 lacking NLS can get entry into nucleus if coexpressed with other viral components, particularly NP and vRNA (23, 45), NLS does not appear to be critically required for nuclear entry of M1 in virus-infected cells. This would imply that in the influenza virus infectious cycle, intranuclear vRNP binding or some other function of NLS may be more critical than the nuclear entry of M1 provided by NLS. Furthermore, M1 causes transcription inhibition and therefore has been implicated in regulation of viral mRNA transcription. Since vRNA is exposed on the surface of vRNP, the RNA binding activity of positive charges encompassing the NLS sequence has been implicated in vRNP binding. However, single-stranded RNA binding activity of M1 is unlikely to provide the specificity required for vRNP binding and transcription inhibition by M1 (12, 27). Our report also show that as expected, when the NLS function was disrupted, M1 expressed alone did not enter the nucleus in cDNA-transfected cells in the absence of other viral proteins (Fig. 9). However, viruses with WT-like growth properties were rescued from M1 mutants containing PTAP, YPDL, 4A+PTAP, and WT+PTAP substitutions (Fig. 8). These results would indicate that the nuclear translocation function provided by the NLS of M1 is not critically required for replication of influenza virus.

Matrix proteins of many enveloped viruses, particularly retroviruses and unsegmented negative-strand RNA viruses, have been shown to contain an L domain which is critically required in budding of viruses from the plasma membrane. The L domain has been thought to function by recruiting a number of host proteins at the budding site, which are required to initiate the budding process (31) and release the virion particles. As indicated earlier, L domains can be grouped into three general classes, namely, PT(S)AP, PPPY (or PPXY), and YPDL (or YXXL), which have been shown to interact with a number of host proteins involved in endocytic vacuolar sorting pathways, such as Tsg101, Nedd4, ubiquitin ligases, and others (reviewed in references 9, 14, 36, and 46). The data presented here show that the H6 domain encompassing the NLS motif can provide the L domain function, since disruption of this domain by mutation of the positively charged residues would cause lethal mutation but replacement of these residues by an L domain, such as PTAP or YPDL, or insertion of PTAP after the mutated residues would fully restore the budding function, and the mutant viruses exhibited the WT phenotype. Although the precise sequence and boundary of the L domain motif of influenza virus M1 are yet to be determined, it is evident that the influenza virus M1 L domain consists at least partly of the positively charged residues of the NLS sequence. Therefore, influenza virus M1 sequences which provide the same function as the other L motifs do not represent a known L motif. Although initially we thought that the YRKL sequence of M1 is likely to be similar to the YPDL (YXXL) motif of EIAV (43, 48, 49), this was not found to be true since the mutation of either Y or L, the critical residues of YPDL, did not affect virus budding. Rather the positively charged residues in the H6 region, which have been implicated in a number of functions, such as NLS, RID, TID, membrane binding, etc., are likely to provide another important function in the budding process. Although the H6 region of M1 provides functions similar to those of PTAP and YPDL, it may not interact with the same host proteins, since different L domain motifs interact with different host proteins, such as Tsg101, Nedd4-like ubiquitin ligases, AP2, and proteins containing SH3 and WW domains, etc. (reviewed in reference 14). It is likely that positively charged residues of the H6 region may interact with a different set of host proteins, which may be involved in apical budding, whereas PTAP and YPDL may interact with protein involved in basolateral budding. Members of our group and others have recently shown that basolateral HA cannot direct influenza virus to bud basolaterally (4, 37), and similarly, apical vesicular stomatitis virus (VSV) G protein cannot direct the VSV to bud from the apical side of polarized epithelial cells (76). It will be important, therefore, to identify the host proteins interacting with M1. Another L domain motif, PPPY, the L motif for VSV M, failed to rescue influenza viruses. The human immunodeficiency virus L motif has been shown to function in a cell-type-dependent manner (11), and all L motifs are not functionally interchangeable (67, 73). For example, human T-cell leukemia virus has both PPPY and PTAP present in tandem, but only PPPY is functional (31). The presence of too many proline residues in PPPY may disrupt the helical structure of H6.

Furthermore, we observed that a single mutation of M1 (R101A) could cause a defect in virus budding, leading to the production of elongated particles as well as VLP-like empty particles. This observation could support the role of M1 as a determinant in particle shape and size as well as in virus budding. Although Roberts et al. (54) have implicated the role of M1 in filamentous particle formation, the mechanism by which filamentous particles are formed in the R101A mutant reported here may be different from that observed with a natural isolate (A/Udorn/301/72) and its mutants obtained against anti-M2 antibodies (54). Moreover, biological properties of the Udorn filamentous particles were also different. For example, the Udorn filamentous particles had essentially the same infectivity as the spherical particles, whereas the R101A mutant was less infectious and contained many empty VLP-like particles.

Formation of filamentous particles by R101A mutants also supports the role of this region in providing L domain function in virus budding. The morphological phenotype of the R101A mutant is strikingly similar to that observed for Moloney murine leukemia virus (M-MuLV) mutants with defects in the L domain (73). Both the R101A influenza virus mutant and M-MuLV mutants exhibited an elongated filamentous shape. Many filaments contain multiple spherical units, a "daisy chain-like" structure, suggesting a defect in releasing spherical particles during budding (Fig. 6C), as was seen with M-MuLV (73) and other retrovirus late mutants (15). Based on their results, Yaun et al. (73) suggested that virions may not bud randomly but rather may bud from preferred sites on the plasma membrane, or budding of one virion may seed for the next in the same site, and a defect in bud release could lead to joining of multiple particles, forming filaments. It was proposed that this process may be coupled with recruitment of host cytoskeletal elements at the preferred site of budding (73). With influenza virus, a cytoskeletal disrupting agent caused an increased release of spherical particles over filamentous particles in MDCK cells (53) and release of virus particles in a few localized regions of the plasma membrane in abortively infected HeLa cells (19).

In summary, we have shown that nuclear entry function of the M1 NLS is not essential for influenza virus replication and that disruption caused by mutation of positively charged residues of NLS can be fully restored by an L motif, such as PTAP and YPDL. Therefore, we conclude that this M1 region provides L domain function in virus budding.

FIG.5


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ACKNOWLEDGMENTS
 
This work was supported by USPHS grants (AI 16348 and AI 41681).

We thank Randip Bisla, Ee Ming Yap, and Shankari Somayaji for their help with DNA preparation and plaque assay and B. M. Sjostrand (BRI EM Core Facility, UCLA) for assistance in electron microscopy.


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FOOTNOTES
 
* Corresponding author. Mailing address: Department of Microbiology, Immunology and Molecular Genetics, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, UCLA School of Medicine, 650 Charles E. Young Dr. So., Los Angeles, CA 90095-1489. Phone: (310) 825-8558. Fax: (310) 206-3865. E-mail: dnayak{at}ucla.edu. Back


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Journal of Virology, June 2003, p. 7078-7092, Vol. 77, No. 12
0022-538X/03/$08.00+0     DOI: 10.1128/JVI.77.12.7078-7092.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.



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