Protein binding sites in nucleation complexes of alfalfa mosaic virus RNA 4

Functional analysis of the 5' untranslated region of potexvirus RNA reveals a role in viral replication and cell-to-cell movement

Cell-to-cell movement of potexviruses requires cognate recognition between the viral RNA, the triple gene block proteins (TGBp1-3) and the coat protein (CP). cis-acting motifs required for recognition and translocation of viral RNA were identified using an artificial potexvirus defective RNA encoding a green fluorescent protein (GFP) reporter transcriptionally fused to the terminal viral sequences. Analysis of GFP fluorescence produced in vivo from these defective RNA constructs, referred to as chimeric RNA reporters, was used to identify viral cis-acting motifs required for RNA trafficking. Mapping experiments localized the cis-acting element to nucleotides 1-107 of the Potato virus X (PVX) genome. This sequence forms an RNA secondary structural element that has also been implicated in viral plus-strand accumulation [Miller, E.D., Plante, C.A., Kim, K.-H., Brown, J.W. and Hemenway, C. (1998) J. Mol. Biol. 284, 591-608]. While replication and movement functions associated with this region have not been separated, these results are consistent with sequence-specific recognition of RNA by the viral movement protein(s). This situation is unusual among viral movement proteins that typically function to translocate RNA between cells in a non-sequence-specific manner. These data support the concept of cis-acting elements specifying intercellular potexvirus RNA movement and thus provide a basis for dissection of RNA-mediated intercellular communication in plants.

Cofolding organizes alfalfa mosaic virus RNA and coat protein for replication

Alfalfa mosaic virus genomic RNAs are infectious only when the viral coat protein binds to the RNA 3' termini. The crystal structure of an alfalfa mosaic virus RNA-peptide complex reveals that conserved AUGC repeats and Pro-Thr-x-Arg-Ser-x-x-Tyr coat protein amino acids cofold upon interacting. Alternating AUGC residues have opposite orientation, and they base pair in different adjacent duplexes. Localized RNA backbone reversals stabilized by arginine-guanine interactions place the adenosines and guanines in reverse order in the duplex. The results suggest that a uniform, organized 3' conformation, similar to that found on viral RNAs with transfer RNA-like ends, may be essential for replication.

Efficient translation of alfamovirus RNAs requires the binding of coat protein dimers to the 3' termini of the viral RNAs

The coat protein (CP) of Alfalfa mosaic virus (AMV) is required to initiate infection by the viral tripartite RNA genome whereas infection by the tripartite Brome mosaic virus (BMV) genome is independent of CP. AMV CP stimulates translation of AMV RNA in vivo 50- to 100-fold. The 3' untranslated region (UTR) of the AMV subgenomic CP messenger RNA 4 contains at least two CP binding sites. A CP binding site in the 3'-terminal 112 nucleotides of RNA 4 was found to be required for efficient translation of the RNA whereas an upstream binding site was not. Binding of CP to the AMV 3' UTR induces a conformational change of the RNA but this change alone was not sufficient to stimulate translation. CP mutant R17A is unable to bind to the 3' UTR and translation in vivo of RNA 4 encoding this mutant occurs at undetectable levels. Replacement of the 3' UTR of this mutant RNA 4 by the 3' UTR of BMV RNA 4 restored translation of R17A-CP to wild-type levels. Apparently, the BMV 3' UTR stimulates translation independently of CP. AMV CP mutant N199 is defective in the formation of CP dimers and did not stimulate translation of RNA 4 in vivo although the mutant CP did bind to the 3' UTR. The finding that N199-CP does not promote AMV infection corroborates the notion that the requirement of CP in the inoculum reflects its role in translation of the viral RNAs.

Spatial determinants of the alfalfa mosaic virus coat protein binding site

The biological functions of RNA-protein complexes are, for the most part, poorly defined. Here, we describe experiments that are aimed at understanding the functional significance of alfalfa mosaic virus RNA-coat protein binding, an interaction that parallels the initiation of viral RNA replication. Peptides representing the RNA-binding domain of the viral coat protein are biologically active in initiating replication and bind to a 39-nt 3'-terminal RNA with a stoichiometry of two peptides: 1 RNA. To begin to understand how RNA-peptide interactions induce RNA conformational changes and initiate replication, the AMV RNA fragment was experimentally manipulated by increasing the interhelical spacing, by interrupting the apparent nucleotide symmetry, and by extending the binding site. In general, both asymmetric and symmetric insertions between two proposed hairpins diminished binding, whereas 5' and 3' extensions had minimal effects. Exchanging the positions of the binding site hairpins resulted in only a moderate decrease in peptide binding affinity without changing the hydroxyl radical footprint protection pattern. To assess biological relevance in viral RNA replication, the nucleotide changes were transferred into infectious genomic RNA clones. RNA mutations that disrupted coat protein binding also prevented viral RNA replication without diminishing coat protein mRNA (RNA 4) translation. These results, coupled with the highly conserved nature of the AUGC865-868 sequence, suggest that the distance separating the two proposed hairpins is a critical binding determinant. The data may indicate that the 5' and 3' hairpins interact with one of the bound peptides to nucleate the observed RNA conformational changes.

The importance of alfalfa mosaic virus coat protein dimers in the initiation of replication

Deletion and substitution mutations affecting the oligomerization of alfalfa mosaic virus (AMV) coat protein (CP) were studied in protoplasts to determine their effect on genome activation, an early step in AMV replication. The CP mutants that formed dimers, CPDeltaC9 and CPC-A(R)F, were highly active in initiating replication with 63-84% of wild-type (wt) CP activity. However, all mutants that did not form dimers, CPDeltaC18, CPDeltaC19, CPC-WFP, and CPC-W, were much less active with 19-33% of wt CP activity. The accumulation and solubility of mutant CPs expressed from a virus-based vector in Nicotiana benthamiana were similar to that of wt CP. Analysis of CP-RNA interactions indicated that CP dimers and CP monomers interacted very differently with AMV RNA 3' ends. These results suggest that CP dimers are more efficient for replication than CP monomers because of differences in RNA binding rather than differences in expression and accumulation of the mutant CPs in infected cells.

Alfalfa mosaic virus: coat protein-dependent initiation of infection

SUMMARY Taxonomy: Alfalfa mosaic virus (AMV) is the type species of the genus Alfamovirus and belongs to the family Bromoviridae. In this family, the tripartite RNA genomes of bromo-, cucumo- and probably oleaviruses are infectious as such, whereas infection with the three genomic RNAs of alfamo- and ilarviruses requires addition to the inoculum of a few molecules of coat protein (CP) per RNA molecule. RNAs 1 and 2 encode the replicase proteins P1 and P2, RNA 3 encodes the movement protein and CP. CP is translated from the subgenomic RNA 4. Physical properties: RNAs 1 (3.65 kb), 2 (2.6 kb) and 3 (2.2 kb) are separately encapsidated into bacilliform particles which are 19 nm wide and 35-56 nm long. In addition, the virus preparations contain spheroidal particles each containing two copies of RNA 4 (0.88 kb). Virus particles contain 16-17% RNA and are mainly stabilized by protein-RNA interactions. The 3'-termini of the viral RNAs contain a homologous sequence of 145 nucleotides that can adopt two alternative conformations: one represents a high-affinity binding site for CP, the other resembles a tRNA-like structure and is required for minus-strand promoter activity. Hosts: AMV mostly infects herbaceous plants, but several woody species are included in the natural host range. The experimental and natural host ranges include over 600 species in 70 families. At least 15 aphid species are known to transmit the virus in the stylet-borne or non-persistent manner. Economic importance: AMV is a significant pathogen in alfalfa and sweet clover and can spread from these forages to neighbouring crops like pepper, tobacco or soybean. The recent introduction of the soybean aphid (Aphis glycines) in the mid-west states of the USA has increased the incidence of AMV in soybean. AMV occurs world-wide in potato and is referred to as 'calico mosaic' because of its characteristic symptoms on the foliage. However, the economic importance of AMV in potato is limited.

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<http://www.socgenmicrobiol.org.uk/JGV/080/1089/0801089A.PDF> review paper; <http://www.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/10010001.htm> host range and physical properties; <http://mmtsb.scripps.edu/viper/1amv.html> structural information.

Stem-loop structure in the 5' region of potato virus X genome required for plus-strand RNA accumulation

Computer-generated thermodynamic predictions and solution structure probing indicated two stem-loop structures, stem-loop 1 (SL1; nt 32-106) and stem-loop 2 (SL2; nt 143-183), within the 5' 230 nt of potato virus X (PVX) RNA. Because the existence of SL1 was further supported by covariation analysis of several PVX strains, the functional significance of this structure was investigated by site-directed mutational analysis in a tobacco protoplast system. In general, mutations that reduced genomic plus-strand RNA accumulation similarly affected coat protein accumulation, indicating that subgenomic plus-strand RNA was also affected. In contrast, minus-strand RNA levels remained relatively unchanged. Mutational analysis of the stem C (SC) region of SL1 indicated that pairing was more important than sequence, which was consistent with the covariation analysis. Alterations that increased length and stability of either SC or stem D (SD) were deleterious to plus-strand RNA accumulation. The formation of internal loop C between SC and SD, as well as specific nucleotides within this loop, were also required. Several modifications were made to the terminal GAAA tetraloop, a motif known for enhanced RNA stability. Both GANA and GAAG motifs resulted in wild-type levels of RNA accumulation. However, a UUCG tetraloop was detrimental, indicating that the sequence of this element was important beyond just providing stabilization of the structure. These data indicate that multiple features of SL1 are critical for accumulation of PVX plus-strand RNA.

RNA determinants of a specific RNA-coat protein peptide interaction in alfalfa mosaic virus: conservation of homologous features in ilarvirus RNAs

Alfalfa mosaic virus (AMV) coat protein and tobacco streak virus (TSV) coat protein bind specifically to the 3' untranslated regions of the viral RNAs and are required with the genomic RNAs to initiate virus replication. A combination of nucleotide substitutions, hydroxyl radical footprinting, and ethylation and chemical modification interference analysis has been used to define the RNA determinants important for the specific binding of the 3'-terminal 39 nucleotides of AMV RNA 3/4 (AMV843-881) to an amino-terminal coat protein peptide (CP26). The results demonstrate that potential phosphate and base-specific contacts as well as ribose moieties protected upon peptide binding cluster in lower hairpin stems and flanking AUGC sequences of the viral RNA, without direct involvement of loop nucleotides. Nucleotides identified in the modification-interference analyses as important for RNA-protein interactions are highly conserved among AMV and the ilarvirus RNAs. This RNA sequence homology, coupled with the recent identification of an RNA binding consensus sequence for AMV and ilarvirus coat proteins, provides a framework for understanding the functional equivalence of AMV and TSV coat proteins in binding RNA and activating virus replication and may explain why heterologous AMV and ilarvirus coat protein-RNA mixtures are infectious.

Structural elements of the 3'-terminal coat protein binding site in alfalfa mosaic virus RNAs

The 3'-terminal of the three genomic RNAs of alfalfa mosaic virus (AIMV) and ilarviruses contain a number of AUGC-motifs separated by hairpin structures. Binding of coat protein (CP) to such elements in the RNAs is required to initiate infection of these viruses. Determinants for CP binding in the 3'-terminal 39 nucleotides (nt) of AIMV RNA 3 were analyzed by band-shift assays. From the 5'- to 3'-end this 39 nt sequence contains AUGC-motif 3, stem-loop structure 2 (STLP2), AUGC-motif 2, stem-loop structure 1 (STLP1) and AUGC-motif 1. A mutational analysis showed that all three AUGC-motifs were involved in CP binding. Mutation of the A- and U-residues of motifs 1 or 3 had no effect on CP binding but similar mutations in motif 2 abolished CP binding. A mutational analysis of the stem of STLP1 and STLP2 confirmed the importance of these hairpins for CP binding. Randomization of the sequence of the stems and loops of STLP1 and STLP2 had no effect on CP binding as long as the secondary structure was maintained. This indicates that the two hairpins are not involved in sequence-specific interactions with CP. They may function in a secondary structure-specific interaction with CP and/or in the assembly of the AUGC-motifs in a configuration required for CP binding.

The 3'-untranslated region of alfalfa mosaic virus RNA 3 contains at least two independent binding sites for viral coat protein

The 3'-termini of the three genomic RNAs of alfalfa mosaic virus contain a common sequence of 145 nucleotides (nt) with a specific binding site for coat protein (CP). This sequence consists of several stem/loop structures interspersed with single-stranded AUGC-motifs; in RNA 3 this folding pattern is extended to a region upstream of the homologous sequence. By band-shift assays a minimum of two specific binding sites for CP were identified near the 3'-end of RNA 3. Site 1 consists of the region between nt 11 and 127 from the 3'-end and contains two AUGC-motifs. Site 2 is located between nt 133 and 208 from the 3'-end in a sequence that is largely unique to RNA 3 and contains also two AUGC-motifs. Deletion studies revealed that the two sites could bind CP independently of each other and permitted the identification of sequence elements that are essential for the activity of each site. By site-directed mutagenesis it was shown that the AUGC-motifs are important for binding of CP to both sites. These binding sites may play a role in the phenomenon that each genomic RNA has to be complexed with a few CP molecules to initiate infection. Later in the replication cycle they may act as origins for the assembly of virus particles.

Nucleotide sequence and structural determinants of specific binding of coat protein or coat protein peptides to the 3' untranslated region of alfalfa mosaic virus RNA 4

The specific binding of alfalfa mosaic virus coat protein to viral RNA requires determinants in the 3' untranslated region (UTR). Coat protein and peptide binding sites in the 3' UTR of alfalfa mosaic virus RNA 4 have been analyzed by hydroxyl radical footprinting, deletion mapping, and site-directed mutagenesis experiments. The 3' UTR has several stable hairpins that are flanked by single-stranded (A/U)UGC sequences. Hydroxyl radical footprinting data show that five sites in the 3' UTR of alfalfa mosaic virus RNA 4 are protected by coat protein, and four of the five protected regions contain AUGC or UUGC. Electrophoretic mobility band shift results suggest four coat protein binding sites in the 3' UTR. A 3'-terminal 39-nucleotide RNA fragment containing four AUGC repeats bound coat protein and coat protein peptides with high affinity; however, coat protein bound poorly to antisense 3' UTR transcripts and poly(AUGC)10. Site-directed mutagenesis of AUGC865-868 resulted in a loss of coat protein binding and peptide binding by the RNA fragment. Alignment of alfalfa mosaic RNA sequences with those from several closely related ilarviruses demonstrates that AUGC865-868 is perfectly conserved; moreover, the RNAs are predicted to form similar 3'-terminal secondary structures. The data strongly suggest that alfalfa mosaic virus coat protein and ilavirus coat proteins recognize invariant AUGC sequences in the context of conserved structural elements.

Coat protein stimulates replication complexes of alfalfa mosaic virus to produce virion RNAs in vitro

Viral replication complexes (RCs) were gradient-purified from cowpea mesophyll protoplasts 21 h after inoculation with alfalfa mosaic virus. These membranous structures incorporate [32P]UMP into double- and single-stranded RNAs in the absence of added template. When coat protein is added prior to the reaction the incorporation in both RNA fractions is stimulated several times. Part of the single-stranded product RNAs are released from the RCs. The stimulation of incorporation in high molecular mass RNAs by coat protein can be mimicked only to a certain extent by addition of a ribonuclease inhibitor or of an excess of viral RNA prior to the reaction. This shows that the coat protein is not only protecting the product of the RCs against degradation by ribonuclease, but that it is stimulating the synthesis and release of viral RNAs from RCs as well. This leads to the hypothesis that with alfalfa mosaic virus some coat protein is necessary for the release of messenger RNA from the RC. The hypothesis explains why the viral genome RNAs, although they are of messenger polarity, cannot start a replication cycle in the absence of coat protein: RCs containing the parental RNAs could be formed but no amplification of them could take place since no messenger RNAs needed for the production of viral polymerase proteins would be released into the cytoplasm.

Evidence that the packaging signal for nodaviral RNA2 is a bulged stem-loop

Flock house virus is an insect virus belonging to the family Nodaviridae; members of this family are characterized by a small bipartite positive-stranded RNA genome. The larger genomic segment, RNA1, encodes viral replication proteins, whereas the smaller one, RNA2, encodes coat protein. Both RNAs are packaged in a single particle. A defective-interfering RNA (DI-634), isolated from a line of Drosophila cells persistently infected with Flock house virus, was used to show that a 32-base region of RNA2 (bases 186-217) is required for packaging into virions. RNA folding analysis predicted that this region forms a stem-loop structure with a 5-base loop and a 13-base-pair bulged stem.

The second amino acid of alfalfa mosaic virus coat protein is critical for coat protein-mediated protection

Transgenic plants expressing the coat protein (CP) of alfalfa mosaic virus (AIMV) are resistant to infection by AIMV. A mutation was introduced into the second amino acid of the cDNA for the CP of AIMV. Three different transgenic tobacco lines expressing the mutant CP and two different transgenic tobacco lines expressing the wild-type CP at similar levels were challenged with AIMV virions and viral RNA. Whereas the lines expressing the wild-type CP were highly resistant to infection by AIMV virions and viral RNA, the lines expressing the mutant CP were susceptible to infection by both. The binding affinity of the mutant and the wild-type CPs for the 3' terminal protein binding site on AIMV RNAs was similar, as determined by electrophoretic mobility shift assay. A mixture of AIMV genomic RNAs 1-3 was infectious on the plants expressing the mutant CP but not on vector control plants or plants expressing the wild-type CP, indicating that the mutant CP can activate the AIMV genomic RNAs for infection. These results demonstrate that the second amino acid of the AIMV CP is critical for protection from AIMV but not for the initial interaction between the AIMV RNA and CP, suggesting that this initial interaction does not play a major role in CP-mediated protection.

cis-acting elements involved in replication of alfalfa mosaic virus RNAs in vitro

A DNA copy of alfalfa mosaic virus (AIMV) RNA3 was transcribed in vitro in two different orientations with T7 RNA polymerase and the transcripts were used as templates for a virus-specific RNA-dependent RNA polymerase (RdRp) purified from AIMV-infected bean plants. Minus-stranded templates were transcribed by the RdRp into subgenomic plus-stranded RNA4. A deletion analysis showed that a sequence in minus-strand RNA3, located between nucleotides -8 and -55 upstream of the initiation site for RNA4 synthesis, was sufficient for subgenomic promoter activity in vitro. Plus-stranded templates were transcribed by the RdRp into full-length minus-stranded copies. A deletion analysis indicated that a sequence located between nucleotides 133 and 163 from the 3'-end of AIMV RNA3 was sufficient to direct the synthesis of minus-stranded products by the RdRp. Thus, the 3'-terminal region of the AIMV RNAs, which contains the binding sites with a high affinity for coat protein, appears not to be involved in recognition of the RNAs by the RdRp in vitro.

Evidence for specificity in the encapsidation of Sindbis virus RNAs

We investigated the interaction of the capsid protein of Sindbis virus with Sindbis viral RNAs and defined a region of the genome that is required for binding in vitro and for packaging in vivo. The binding studies were performed with purified capsid protein immobilized on nitrocellulose and 32P-labeled RNAs transcribed in vitro from viral and nonspecific cDNAs. Genomic and defective interfering (DI) RNAs bound capsid protein significantly better than either the subgenomic (26S) RNA or nonspecific RNAs. Transcripts prepared from either truncated or deleted cDNAs were used to define the segment required for binding. This segment, which is represented twice in DI RNA, lies between nucleotides 746 and 1226 of the genomic RNA and is within the coding region of the nonstructural protein nsP1. Insertion of a domain covering these sequences into a nonviral RNA was able to convert it from a background level of binding to an activity that was 80% that of the Sindbis virus DI RNA. We analyzed DI RNA transcripts in detail because they could be studied not only for the ability to bind capsid protein in vitro but also for the ability to be replicated and packaged in vivo in the presence of helper virion RNA. The results obtained with three DI RNAs are reported. One (CTS14), which has one copy of the binding domain, bound efficiently to capsid protein in vitro and was packaged in vivo as measured by amplification on passaging. In contrast, a DI RNA (CTS1) which lacked this region did not bind to capsid protein and was not detected on passaging. By using lipofectin (P. L. Felgner, T. R. Gadek, M. Holm, R. Roman, H. W. Chan, M. Wenz, J.P. Northrop, G. M. Ringold, and M. Danielson, Proc. Natl. Acad. Sci. USA 84:7413-7417, 1987) to enhance RNA uptake, we were able to demonstrate that CTS1 RNA was replicated in the transfected cells. It was replicated to the same level as another DI RNA (CTS253) which has only the 3' 279 nucleotides of the binding domain and these are located near the 3' terminus of the RNA. CTS253 bound capsid protein to an intermediate level but was amplified on passaging. The binding studies and the in vivo packaging data, taken together, provide strong support for the conclusion that there is a specific capsid recognition domain in Sindbis virus RNA that plays a role in nucleocapsid assembly.

Transgenic tobacco expressing tobacco streak virus or mutated alfalfa mosaic virus coat protein does not cross-protect against alfalfa mosaic virus infection

Transgenic tobacco plants expressing the coat protein (CP) genes of tobacco streak virus (TSV) and alfalfa mosaic virus (AIMV) were used in studies on cross-protection and genome activation. Plants expressing the TSV CP gene were highly resistant to infection with TSV nucleoproteins but were susceptible to infection with AIMV nucleoproteins. Moreover, these plants could be infected with a mixture of AIMV RNAs 1, 2, and 3 in contrast to the nontransformed control plants. This demonstrates that the endogenously produced TSV CP is able to activate the AIMV genome but does not cross-protect against this virus. Conversely, it was shown that plants expressing the AIMV CP gene did not resist TSV infection. Transgenic tobacco plants transformed with an AIMV CP gene with a frame-shift mutation in the reading frame were found to accumulate viral transcripts to a level similar to that obtained in plants expressing a wild-type AIMV CP gene. However, these plants did not produce detectable amounts of viral protein and showed no resistance to infection with AIMV nucleoproteins in contrast to transgenic plants accumulating wild-type AIMV CP. This demonstrates that it is the CP that is responsible for cross-protection in transgenic plants and not the chimeric CP mRNA.

Biologically active transcripts of cloned DNA of the coat protein messenger of two plant viruses

To initiate infection, a mixture of the three genomic RNAs of alfalfa mosaic virus (AIMV) has to be supplemented with a small amount of coat protein or RNA 4, the subgenomic messenger for coat protein. The possibility to replace RNA 4 in the inoculum by in vitro synthesized transcripts of a cloned DNA copy of the coat protein cistron was investigated using the SP6 transcription system. Transcripts with or without the cap structure m(7)G(5')ppp(5')G were both translated in vitro in viral coat protein, but only capped transcripts yielded an infectious mixture when added to the AIMV genomic RNAs. This indicates that the cap structure is essential to the in vivo translatin of RNA 4. Similar results were obtained with RNAs transcribed in vitro from a DNA copy of the putative coat protein cistron of tobacco streak virus (TSV). re]19850822 rv]19851203 ac]19860114.

Complete nucleotide sequence of tobacco streak virus RNA 3

Double-stranded cDNA of in vitro polyadenylated tobacco streak virus (TSV) RNA 3 has been cloned and sequenced. The complete primary structure of 2,205 nucleotides reveals two open reading frames flanked by a leader sequence of 210 bases, an intercistronic region of 123 nucleotides and a 3'-extracistronic sequence of 288 nucleotides. The 5'-terminal open reading frame codes for a Mr 31,742 protein, which probably corresponds to the only in vitro translation product of TSV RNA 3. The 3'-terminal coding region predicts a Mr 26,346 protein, probably the viral coat protein, which is the translation product of the subgenomic messenger, RNA 4. Although the coat proteins of alfalfa mosaic virus (A1MV) and TSV are functionally equivalent in activating their own and each others genomes, no homology between the primary structures of those two proteins is detectable.

Complete nucleotide sequence of alfalfa mosaic virus RNA3

A full-length cDNA clone of alfalfa mosaic virus (AMV) RNA3 was prepared and sequenced. The 2,037 base sequence contains two open reading frames of 903 and 666 nucleotides that code for a 32,400 dalton protein (32.4K protein) and the 24,380 dalton coat protein, respectively. A 5'-noncoding sequence of 240 bases preceeding the 32.4K protein contains homologous regions that may have a function in its translation. The intercistronic junction is 49 bases long, the last 36 bases representing the 5'-end of the subgenomic RNA4. The remaining 179 bases comprise the 3'-terminal noncoding sequence.

Coat protein binding sites on RNA 1 of alfalfa mosaic virus

The largest genome segment, RNA 1, of alfalfa mosaic virus forms complexes with viral coat protein. These complexes were subjected to digestion with ribonucleases T1 or A and filtered onto Millipore filters. Specific fragments were collected from the filters by phenol extraction. After electrophoretic separation in denaturing polyacrylamide gels, these fragments were sequenced. Besides extracistronic fragments originating from the 3'-terminal region of RNA 1, fragments were found originating from an intracistronic region of the RNA. A striking phenomenon is that the intracistronic fragments were not found when ribonuclease A was used to degrade RNA/protein complexes. The findings are in agreement with the postulation of Houwing and Jaspars (1978), that a conformational change at the 3' ends of the genome RNAs induced by the coat protein is a prerequisite to start an infection cycle.