Journal of General Virology (1994), 75, 3742. Printed in Great Brita#l 37 A small percentage of influenza virus M1 protein contains zinc but zinc does not influence in vitro M 1 - R N A interaction Christine Elster, ~ Eric Fourest, 2 Florence Baudin, ~ Kjeld Larsen, ~ Stephen Cusack 1 and Rob W. H. Ruigrok 1. 1 E M B L Grenoble Outstation, c / o I L L , B P 156, 38042 Grenoble Cedex 9 and 2 C E N - G / D B M S / T S V , 38041 Grenoble Cedex, France B P 85X, A peptide containing the C C H H motif, the putative zinc-binding sequence o f influenza virus M1 protein, was found to bind zinc in a one-to-one complex with the characteristics of a typical zinc-binding peptide. Intact influenza virus also contained zinc and we show that this zinc is bound to the M1 protein in the virus. However, only a small proportion of M1 contained zinc: 4 % in virus and 6 to 9 % in isolated protein. One strain, B/Yamagata/16/88, consistently contained more zinc: 15 to 2 0 % both in virus and in isolated protein. We also determined the RNA binding and transcription inhibition activities of various M1 proteins and found that the zinc content of M1 had no influence on either activity. We suggest that the zinc in M1 has a structural role in the virion other than nucleic acid binding. Introduction C y s X a a ~ - C y s X a a 7 His-Xaa~ His ( C C H H motif) (residues 148 to 162 of A / P R / 8 / 3 4 M1 protein; Allen et al., 1980), first remarked upon by Wakefield & Brownlee (1989), which could be involved in R N A binding. This C C H H motif is situated in a part of the M1 sequence that may be involved in transcription inhibition (Ye et al., 1989). Zinc-binding sequences have been implicated in specific protein-nucleic acid interactions and protein dimerization domains (see references in Discussion). In this paper we describe the zinc-binding activity of a 27 amino acid peptide containing the C C H H motif and have determined the zinc content of intact influenza virus and purified M 1. We further show that the zinc content of M1 does not influence the in vitro R N A binding and transcription inhibition activities of M1. Influenza viruses are enveloped viruses with a segmented negative strand R N A genome. Each v R N A segment is complexed with the major RNA-binding protein nucleoprotein (NP) and carries a copy of the polymerase complex. These structures, called ribonucleoprotein particles (RNPs), are independent active transcription units. The total genome consists of eight RNPs which are contained within a shell of M1 protein which lines the inside of the viral lipid bilayer. Embedded in this lipid bilayer are the viral glycoproteins which are essential for entry into and release from the host cell. The structure of the virion suggests an important role for the M 1 protein. M 1 may interact with the cytoplasmic tails of the glycoproteins, the lipid membrane and the RNPs and so form the 'glue' between them. Interaction of M 1 with lipid has been shown in intact virus using light-activated cross-linking (Gregoriades & Frangione, 1981) and also in vitro using isolated M1 and liposomes (Bucher et al., 1980). Contact between M1 and the glycoproteins has not yet been shown but interaction of M1 with RNP is suggested by the fact that purified M1, when added to transcribing RNPs, inhibits transcription (Zvonarjev & Ghendon, 1980; Ye et al., 1989). hi vitro interaction of M 1 with R N A has been shown with filterbinding assays and a blotting technique (Wakefield & Brownlee, 1989; Ye et al., 1989). The primary sequence o f all influenza A and B M1 proteins contains the putative zinc-binding sequence 0001-1904 © 1994 SGM Methods Virus and M1 protein. InfluenzavirusesA/PR/8/34, B/Beijing/1/87 and B/Yamagata/16/88 were grown in embryonated hen's eggs and obtained in purified form from Pasteur-Mrrieux, Marcy L'Etoile, France. M1 protein was isolated from spikeless virus. Spikes were removed by bromelain digestion (Brand & Skehel, 1972) which was stopped by addition of 100 mM-iodoacetamide. Spikeless virus was then purified by pelleting through 14% sucrosein PBS. The virus was then disrupted with 1% Triton X-I00 in PBS and centrifugedon a 10 to 30 % continuousglycerolgradientin PBS (SW41rotor, 36000 r.p.m., 4 °C, 16 h). M1 was collectedfrom the upper fractions of the gradient and stored immediatelyat -20 °C. The purity was judged to be higher than 90% by PAGE (Fig. 1). Virus protein concentrationswere determined by the Lowry method (Lowry et al., 1951) using BSA as a standard. The concentration of isolated M 1 protein was determinedwith the Lowry and the Bradford C. Elster and others 38 1 2 3 4 5 6 HA NP MI Fig. 1. Polyacrylamide gel of intact influenza viruses (lanes 1 to 3) and isolated M1 proteins (lanes 4 to 6) used in this study, non-reducing conditions. Lanes 1 and 4: A/PR/8/34; lanes 2 and 5 B/Beijing/1/87 ; lanes 3 and 6: B/Yamagata/16/88. The gel was stained with Coomassie blue G250. HA, Haemagglutinin. (1976) assays, both using BSA as standard, and by absorbance measurements using the known amino acid composition of A/PR/8 M 1 and the molar extinction coefficients of Tyr and Phe. These three methods yielded values within 20 % of each other and any one of these methods was used throughout this work depending on concentration and volume of the protein solutions. Peptide studies. A 27-residue peptide with the A/PR/8/34 M1 sequence EVAFGLVCATCEQIADSQHRSHRQMVT (MP3) was synthesized using the solid phase technique at EMBL, Heidelberg, Germany. Peptide concentrations were determined by weighing out powder: the factor between powder weight and peptide concentration was determined by amino acid analysis. All cysteines in a fresh peptide solution were reduced but the solutions had to be used immediately after preparation in order to avoid oxidation since oxidized peptide did not bind metals. Metal binding studies were performed in 20 mMHEPES, 50 mM-NaC1 pH 7.0. Absorption spectra between 700 and 250 nm were measured in a Kontron Uvikon 941 spectrophotometer. Cobalt titration was performed by adding 1 gl of a 10 mM-CoCI 2 solution to 1 ml peptide solution (60 gM) from 0 to 120 gM-Co~+ in 10 gM steps. The dissociation constant for the peptide/Co -"+ complex was determined using a least-square model fitting approach. Atomic absorption spectroscopy. The amount of zinc complexed with virus and purified proteins was determined after extensive dialysis against PBS by atomic absorption spectroscopy using a Perkin Elmer model 2380 single-beam atomic absorption spectrophotometer. An ai~acetylene flame was used and the absorption was measured at 213-9 nm. The measurements were calibrated against a standard zinc solution in PBS. PBS without zinc was used for zero point calibration. Measurement in PBS diluted 20-fold, in order to try to reduce the noise level, gave very similar results. Typical concentrations used were I0 mg/ml for virus and 1 mg/ml for M1 and RNP. The detection limit for zinc was about 10 ng/ml. Quantification of other metal ions was carried out at the following wavelengths : 248.3 nm for Fe z+, 232 nm for Ni 2+ and 324.8 nm for Cu 2+. RNA binding assays. Segment 8 viral RNA was produced by in vitro run-off synthesis using T7 RNA polymerase. Prior to transcription, the plasmid DNA (pHgaNS, a gift from Mark Krystal, Mount Sinai School of Medicine, New York, N.Y., U.S.A.) was digested with the restriction enzyme HgaI, which defines the 3' terminus of the transcripts as nucleotide + 890 of the gene. Digested DNA was used as template to produce NS vRNA (Davanloo et al., 1984). The binding constant of NS vRNA to M 1 was determined by a nitrocellulose binding assay. The standard reaction buffer for the binding assay was 10 mM-HEPES pH 8.0, 25 mM-NaC1, 5 mM-MgCI 2 and 2-5 mM-DTT. The reaction volume was 45 gl. The M 1 protein was incubated with the a"-P-labelled vRNA (30 pmol) for 30 min at 20 °C and filtered through nitrocellulose filters (Whatman, 0.45 pm pore size). The RNA complexed with M1 bound to the filters and could be detected by scintillation counting. Since the amount of RNA used was extremely small, the M1 concentration at 50% RNA retention is taken to be the dissociation constant K~j. Transcription inhibition assay. For transcription assays, glycerol gradient-purified RNPs (Honda et al., 1988) were used. bl vitro transcription was carried out at 30 °C for 2 h. Standard reaction mixture (Honda et al., 1986; Ishihama et al., 1986) contained 50 mMTris-HC1 pH 7"8, 30 mM-NaC1, 5 mM-MgCI~, 1 mM-DTT, 200 gMNTPs, 10 ~tCi [c~-3~P]UTP, 200 gM-ApG as primer and 0.015 gM-RNP (based on NP concentration and assuming 75 copies of NP per RNP on average). The reaction was stopped by addition of 50 gl 8 % sodium pyrophosphate and RNA precipitation was carried out by addition of 100 gl of 10% TCA. Insoluble material was collected on Whatman G F / C filters, extensively washed with 20ml 10% TCA and the radioactivity was measured by scintillation counting. Results Z i n c binding by C C H H - b o x peptide The absorption spectrum of the Co~+/peptide complex w i t h v a r i o u s a m o u n t s o f C o ~'+ is s h o w n in F i g . 2(a). T h e s p e c t r u m is c h a r a c t e r i s t i c f o r t e t r a h e d r a l l y c o o r d i n a t e d C o ~'+ w i t h p e a k a b s o r b a n c e s at 284 n m (e = 3680 M-1. c m 1) a n d 6 2 0 n m (e=570M 1.cm-1). W h e n the a b s o r b a n c e at 2 8 4 n m is p l o t t e d a g a i n s t the C o .-'+ c o n c e n t r a t i o n (Fig. 2b), a l i n e a r i n c r e a s e in signal is o b s e r v e d until e q u i m o l a r a m o u n t s o f C o .'.+ a n d p e p t i d e are r e a c h e d , s u g g e s t i n g a 1:1 C o 2 + / p e p t i d e c o m p l e x . L e a s t - s q u a r e c u r v e - f i t t i n g suggests a K d o f 0.2 gM at p H 7.0. A d d i t i o n o f Z n 2+ to t h e C o 2 + / p e p t i d e c o m p l e x leads to a d e c r e a s e in the a b s o r b a n c e a n d since e q u i m o l a r a m o u n t s o f Z n 2+ c o m p l e t e l y d i s p l a c e t h e C C +, the K d f o r Z n 2+ m u s t be c o n s i d e r a b l y l o w e r t h a n t h a t f o r C o 2+. T h e s h a p e o f the a b s o r p t i o n s p e c t r u m , t h e m o l a r a b s o r b a n c e s a n d t h e K d are v e r y s i m i l a r to t h o s e o f o t h e r Z n 2+b i n d i n g p e p t i d e s , s u c h as t h o s e d e r i v e d f r o m r e t r o v i r a l nucleic acid-binding proteins, alcohol dehydrogenase a n d a l a n y l - t R N A s y n t h e t a s e ( G r e e n & Berg, 1989; Berg, 1993; B e r g m a n et al., 1992; M i l l e r et al., 1991). Z h w content in virus and isolated M 1 T h e z i n c c o n t e n t o f p u r i f i e d i n t a c t virus, spikeless virus, i s o l a t e d M 1 a n d R N P w a s d e t e r m i n e d by a t o m i c a b s o r p t i o n s p e c t r o s c o p y . T h e results ( T a b l e 1) c l e a r l y s h o w t h a t t h e r e is zinc in i n f l u e n z a virus. T h e zinc is n o t a s s o c i a t e d w i t h p u r i f i e d R N P o r w i t h t h e spikes b u t w a s found associated with purified M1 protein. When e x p r e s s e d as m o l e s o f z i n c p e r m o l e o f M 1 it b e c o m e s c l e a r t h a t o n l y 4 to 6 % o f the M 1 m o l e c u l e s c o n t a i n a Zinc in it~uenza virus M1 protein 39 Table l. Zinc content of influenza virus and isolated protein components 0.25 0.2 0-15 e~ © e~ 0.1 < 0.05 -0.05 i i !i i 300 200 0.3 i (b) I 400 500 600 Wavelength (nm) i i i i i 700 i i 800 ] - - 0-2 0.1 0.0 20~ i 401 i 60L ~ 810 L i i i 100 Co 2+ (BM) + i 0-3 i i i i i i O rl Sample* Intact virus A/PR/8/34 B/Beijing/1/87 B/Yamagata/16/88 Batch 1 Batch 2 Spikeless virus:~ A/PR/8/34 B/Beijing/1/87 B/Yamagata/16/88 Isolated M1 protein A/PR/8/34 B/Beijing/1/87 B/Yamagata/16/88 Isolated RNP A/PR/8/34 Zinc (rig per mg sample)~ Mole zinc per mole MI$ 13"1 ± 1"0 (n = 7) 13"8±0"7 (n = 3) 0'042±0"003 0"044±0"002 46.4_+ l'3 (n = 3) 63-5 ( n = 1) 0"148±0'004 0"203 70-5 69 239 221 _+40 (n = 2) 149_+11 (n = 2) 438+101 (n = 2) 0-059 0.058 0"198 0"092 0.062 0'182 10±18 (n = 5)§ *The seven determinations of intact A/PR/8 virus and three of intact B/Beijing virus were independent experiments using virus from three and two different batches respectively. The measurements on B/Yamagata virus were also done on virus from two separate batches, as indicated. ?Amounts of virus and spikeless virus are given as mg of protein. :~Assuming that all zinc is associated with M 1 and that 13 % of viral protein is M1. This amount of M1 is based on physical measurements on monodisperse, egg-grown virus (Ruigrok et al., 1984; Cusack et al., 1985). Virus contains 50% spikes, 25% lipid and 25% internal proteins (NP, M1 and polymerases) and spikeless-virus protein is assumed to be 50% M1. §This value is ng zinc per mg NP; this corresponds to 0-002 ions of zinc per molecule NP and to 0.15 zinc ions per RNP (assuming on average 75 NP per RNP) and consequently to 0.15 zinc ions per polymerase complex. The determined amount of Zn is at the limit of detection, hence the large relative standard deviation. 0-2 0-1 0-00 i 210 i i i i 40 60 Zn 2+ (BM) C m i ; 8 m L 100 Fig. 2. Metal binding by peptide MP3. (a) Absorption scans of MP3 with various amounts of CoCI~. The curves correspond to 60 BM-MP3 plus 0, 10, 20, 30, 40, 50, 60, 70, 80 and 90 gM-CoCI~. (b) Absorbance at 284 nm of 60 gM-MP3 as a function of CoCI~ concentration. (c) Absorbance of a 60 BM-Co2+/MP3 complex as a function of added concentration of ZnCla. The residual density after complete displacement of the cobalt by the zinc is probably due to light-scattering. The spectra showed a sloping, f?atureless line with none of the characteristic absorption peaks of the cobalt complex. zinc ion in intact and spikeless virus of A / P R / 8 and B/Beijing compared with 15 to 20% in B/Yamagata. The fact that similar amounts of zinc per M 1 molecule are found in virus and in purified M 1, and the covariation of zinc content in intact virus and purified M1 of A / P R / 8 and B/Beijing virus on the one hand and B/Yamagata on the other, are strong arguments that zinc is indeed associated only with M 1. We were surprised to find that B/Yamagata contained more zinc than B/Beijing and A / P R / 8 (of which three different batches were tested always with the same result). We therefore tested a second batch of B/Yamagata that was produced a year later and again found a significantly higher zinc content, suggesting that this difference between B/Yamagata and the other two viruses is real. Oxford & Perrin (1975) also detected zinc in a purified influenza virus preparation (3 ng zinc per mg viral protein) and suggested that it could be associated with the viral polymerases. However, the amount of zinc in purified R N P determined here is at or just below the reliable detection level and suggests that there cannot be more than 0-15 ions of zinc per polymerase complex (Table 1). We tested for the presence of other divalent metal ions and found no significant amounts of copper, nickel or iron. The zinc in isolated M1 could not be removed by C. Elster and others 40 0.8 I I fill I I I I I Illl I I I I I Illl I I I I ....... f I l[ll 0.6 o 0.4 "" O.2 , 0"0 O, ,~,l 1 P, 1 •i ..... I ........ 10 M1 (nM) 100 1000 Fig. 3. RNA-binding activity of purified M1 proteins. MI was mixed with segment 8 vRNA and filtered over a nitrocellulose membrane. The fraction of retained RNA is shown. The experiments were performed on the same day with fresh M I and a single RNA preparation. Experiments showed more variation when different RNA preparations were used and varied with the age of the MI preparation. (1) M 1/A/PR/8/34; (C)) M 1/B/Beijing/1/87; ( x ) M 1/B/Yamagata/88. Table 2. Transcription inhibition activity of MI and peptide MP3 Sample M1, A/PR/8 M1, B/Beijing MI, B/Yamagata MP3 MP3/ZnC1z ZnCI~ ZnC12 Concentration (pM) 1 10 1 10 1 10 65 65/33 22 44 Transcription (%)* 70+ 14 (n = 4) 17_+5 (n = 3) 69_+19 (n = 5) 22_+14 (n = 5) 69_+16 (n = 5) 22_+13 (n = 3) 108_+12 (n = 3) 127_+17 (n = 2) 43 (n = 1) 23 _+5 (n = 6) *The 100% valuewas independentlydetermined for eachexperiment in the absence of M1 or peptide. extensive dialysis against 10 mM-EDTA or against a 100-fotd dilution o f a saturated solution of 1,10phenanthroline, suggesting that the zinc is tightly bound and possibly not accessible to solvent. RNA-binding activity of M1 The vRNA-binding activity of M 1 was determined using a filter binding assay. We found that v R N A binding did not vary with the M1 zinc content (Fig. 3). R N A binding by B / Y a m a g a t a M1 was as strong as that by A / P R / 8 and B/Beijing M1, although it contained four times more zinc. The average K d values for R N A binding by M 1 are: 21 ± 6 nM (n ----7) for A / P R / 8 , 24 ___5 nM (n = 4) for B/Beijing and 17±6rim (n = 3) for B/Yamagata. Wakefield & Brownlee (1989) found 50% retention of R N A at a concentration of 30 nM M1 from A / P R / 8 . Dialysis of M 1 against E D T A did not remove zinc (see above) and did not lead to a change in R N A binding. We also tested the RNA-binding activity of B/Beijing M 1 that had been isolated and purified in the presence of 2mM-DTT and 100pM-ZnCl~. In this type of M1 preparation it was found that after extensive dialysis against PBS between 40 and 100 % of M1 molecules contained zinc (three experiments). Using this zincloaded M1 we still found a K d of 25 riM. When R N A was incubated with the zinc-binding peptide MP3, in the presence or absence of zinc, the R N A was not retained on the filter. Gel retardation experiments also indicated no binding of this peptide to R N A (data not shown). In vitro transcription inhibition The transcription inhibition activities of purified M 1 and peptide MP3 are shown in Table 2. As with the RNAbinding, the transcription inhibition activity of all three M1 preparations was very similar and apparently independent of the zinc content. MP3 did not inhibit transcription, either in the presence or absence of zinc. Interestingly, zinc by itself did inhibit transcription probably by poisoning the polymerase. This inhibition was overcome by adding the zinc-binding peptide, effectively removing the free zinc. This finding is a further indication that the zinc in influenza virus is associated with M1 and not with the polymerase as suggested by Oxford & Perrin (1975). We found that several divalent cations could inhibit the polymerase activity to different extents in the order ZnC12 > MnC12 > CaC12 > CoC12. R N P that had been dialysed against E D T A lost all its polymerase activity, which could be completely restored by the addition of 1.5 mM-MgCI~ or to a lesser extent by MnC12 (25 % restoration with 50 pM but inhibition at 1 mM). Discussion Generally, zinc-binding sequences in proteins are involved in specific nucleic acid recognition, protein dimerization or otherwise holding together protein loops; zinc can also have a catalytic function in enzymes (Schwabe et al., 1990; Cunningham et al., 1991 ; Kaptein, 1991 ; Vallee & Auld, 1990). We show here that influenza virus M1 protein does contain zinc but that its zinc content is not stoichiometric and does not influence its interaction with v R N A as measured by filter binding assays and in vitro transcription inhibition. The peptide containing the zinc-binding sequence did not bind to R N A or inhibit transcription. Therefore, we think that the zinc in M1 is not involved in an RNA-binding structure and must have some other function. Z i n c in influenza virus M 1 protein Retrovirus nucleocapsid proteins (NC) contain two stretches of a conserved sequence Cys-Xaa2-Cys-Xaa4His-Xaa4-Cys which have been shown to bind zinc both in the isolated peptide and in the protein (Green & Berg, 1989, 1990). Some purified retroviruses contain zinc at a stoichiometry of two zinc ions per copy of NC (Bess et al., 1992). However, in one retrovirus, avian myeloblastosis virus, only 2 % of NC molecules contain zinc (Jentoft et al., 1988), analogous to the case of the zinc in influenza virus M 1. Only a small proportion of M1 in influenza virus contains zinc, about 4 % in A / P R / 8 and B/Beijing and between 15 and 20 % in B/Yamagata. This could equally mean that 4% (15%) of the virions have fully zincoccupied M1 (Zn/M1) or that every virion has 4% (15%) of its M1 occupied with zinc. If zinc has an influence on the conformation of M1, one could imagine that a virus particle with 100% Zn/M1 might appear different from a particle with no Z n / M 1. In fact, electron microscopy of negatively stained influenza virus has shown two separate types of virus with different polymerization forms of M l: virus with 'fingerprints' which are arrays of single lines of protein with units spaced 4 nm apart, and virus with 'coils' which are paired lines of protein with the same spacing between the lines within a pair but with a larger spacing between adjacent pairs (Ruigrok et al., 1989). We examined the A / P R / 8 virus used in the present study and found that less than 0"1% of particles had coils, suggesting that the particles with coils are not the hypothetical virions with 100% Zn/M1. The two type B virus strains did not contain any particles with coils. Further, we found no morphological differences between B/Yamagata and B/Beijing virus, both showing only one type of virus having 'fingerprints' with similar spacings between the lines and the subunits. Therefore, we propose that, with respect to zinc content, two different types of virus particles do not exist and that every virion contains M1 both with and without zinc. We suggest that Zn/M1 may occupy a position in the virus different from that of M1 without zinc. Electron microscopy of the fine structure of the M1 layer in the virus suggests that it is not homogeneous (Ruigrok et al., 1989). An exciting hypothesis is that the molecules of M 1 that surround the few copies of M2 present in the viral membrane (Zebedee & Lamb, 1988) are different from the rest of the M 1. Interaction between M 1 and M2 has been suggested by Zebedee & Lamb (1989) who found that virus growth restriction by anti-M2 antibodies could be overcome by mutations in M1. At present we can only speculate why there is relatively more of the zinc-binding form of M1 in B/Yamagata than in A / P R / 8 and B/Beijing. The M1 amino acid sequences of B/Yamagata and B/Texas/88, a B/Beijing- 41 like strain, differ by only one residue (Paul Rota, personal communication) which is not near the CCHH motif. The two type B viruses are in two separate cocirculating lineages (Rota et al., 1990) and the difference between them lies largely in the sequence of the haemagglutinin HA1 region and in the sequence of the part of RNA segment 6 that codes for both the stalk of neuraminidase and for NB, the type B virus homologue of type A virus M2 (Burmeister et al., 1993). If Zn/M1 does surround M2 (or NB), then differences in NB could possibly lead to a requirement for more Zn/M1. To test this, more sequence information on segment 6 and zinc determinations of type B strains would be needed. The presence of two different forms of M 1 in influenza virus would not be unique in the negative-strand RNA virus group. Two biochemically different kinds of vesicular stomatitis virus M protein, one membranous and one cytoplasmic, were recently found after expression of M in HeLa cells (Chong & Rose, 1993). Two different kinds of M in rabies virus also exist, one palmitoylated and one unmodified (Gaudin et al., 1991). Recently, two antigenically different types of M were found in Sendai virus (de Melo et al., 1992) and functional differences between M proteins were found in subacute sclerosing panencephalitis virus and its measles parental virus (Hirano et al., 1992). 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