Specificity of RNA and coat protein interaction in alfalfa mosaic virus and related viruses

Well-defined coat protein binding sites were found to be present on the genomic RNAs of AlMV and TSV. In view of the regulatory importance of these sites in virus multiplication, the possibility that nonrelated proteins also were able to interact with these sites was investigated. The coat proteins of TSV, BMV, CMV, and SBMV recognize specific sites on AlMV RNA 1. The significance of these sites in virus multiplication is discussed. No specific binding sites were found with TMV coat protein or the nonviral proteins ovalbumin, myoglobin, and lysozyme. Moreover, the ability of AlMV coat protein to recognize specific sites on the heterologous RNAs of TSV, BMV, bacteriophage MS2, and Escherichia coli was tested. No specific sites were found with MS2-RNA. However, specific binding sites were found with BMV-RNA 3 and, unexpectedly, with E. coli 16 S ribosomal RNA. From these data it was concluded that binding of AlMV and TSV coat proteins to their genomic RNAs is a specific process. However, the binding of coat protein to BMV-RNAs and to ribosomal RNAs may result from secondary folding that may have been conserved for other purposes throughout evolution of the RNAs.     

cis-acting elements at opposite ends of the Citrus tristeza virus genome differ in initiation and termination of subgenomic RNAs

Citrus tristeza virus (CTV), a member of the Closteroviridae with a plus-stranded genomic RNA of approximately 20 kb, produces 10 3'-coterminal subgenomic (sg) RNAs that serve as messenger (m)RNAs for its internal genes. In addition, a population of 5'-terminal sgRNAs of approximately 700 nts are highly abundant in infected cells. Previous analysis demonstrated that the controller elements (CE) are responsible for the 3'-terminal mRNAs and the small 5'-terminal sgRNAs differ in the number of additional sgRNAs produced. A feature of both types of CE is production of 5'- and 3'-terminal positive-stranded sgRNAs, but the 3' CEs additionally produce a negative-stranded complement of the 3'-terminal mRNAs. Here, we found that the termination (for 5'-terminal sgRNAs) and initiation (for 3'-terminal sgRNAs) sites of the 5' vs. the 3' CEs occur at opposite ends of the respective minimal active CEs. The initiation site for the 3' CE of the major coat protein gene, and probably those of the p20 and p23 genes, was outside (3' in terms of the genomic RNA) the minimal unit, whereas the termination sites were located within the minimal CE, 30-50 nts upstream of the initiation site (referring to the positive-strand sequence). In contrast, the initiation site for the 5' CE was in the 5' region of the minimal unit, with the termination sites 20-35 nts downstream (referring to the positive-strand sequence). Furthermore, the CEs differ in initiation nucleotide and response to mutagenesis of that nucleotide. The 3' CE initiates sgRNA synthesis from a uridylate, whereas the 5' CE initiates from a cytidylate. We previously found that the 3' CEs were unusually tolerant to mutagenesis of the initiation sites, with initiation proceeding from alternative sites. Mutagenesis of the initiation site of the 5' CE prevented synthesis of either the 5'- or 3'-terminal sgRNAs. Thus, the cis-acting elements at opposite ends of the genome are remarkably different, perhaps having arisen from different origins and or with different functions in the life cycle of this virus.     

Replication of an incomplete alfalfa mosaic virus genome in plants transformed with viral replicase genes

RNAs 1 and 2 of alfalfa mosaic virus (AIMV) encode proteins P1 and P2, respectively, both of which have a putative role in viral RNA replication. Tobacco plants were transformed with DNA copies of RNA1 (P1-plants), RNA2 (P2-plants) or a combination of these two cDNAs (P12-plants). All transgenic plants were susceptible to infection with the complete AIMV genome (RNAs 1, 2, and 3). Inoculation with incomplete mixtures of AIMV RNAs showed that the P1-plants were able to replicate RNAs 2 and 3, that the P2-plants were able to replicate RNAs 1 and 3, and that the P12-plants were able to replicate RNA3. Initiation of infection of nontransgenic plants, P1-plants, or P2-plants requires the presence of AIMV coat protein in the inoculum, but no coat protein was required to initiate infection of P12-plants with RNA3. Results obtained with P12-protoplasts supported the conclusion that coat protein plays an essential role in the replication cycle of AIMV RNAs 1 and 2.     

Two cellular proteins that interact with a stem loop in the simian hemorrhagic fever virus 3'(+)NCR RNA

Both full-length and subgenomic negative-strand RNAs are initiated at the 3' terminus of the positive-strand genomic RNA of the arterivirus, simian hemorrhagic fever virus (SHFV). The SHFV 3'(+) non-coding region (NCR) is 76 nts in length and forms a stem loop (SL) structure that was confirmed by ribonuclease structure probing. Two cell proteins, p56 and p42, bound specifically to a probe consisting of the SHFV 3'(+)NCR RNA. The 3'(+)NCR RNAs of two additional members of the arterivirus genus specifically interacted with two cell proteins of the same size. p56 was identified as polypyrimidine tract-binding protein (PTB) and p42 was identified as fructose bisphosphate aldolase A. PTB binding sites were mapped to a terminal loop and to a bulged region of the SHFV 3'SL structure. Deletion of either of the PTB binding sites in the viral RNA significantly reduced PTB binding activity, suggesting that both sites are required for efficient binding of this protein. Changes in the top portion of the SHFV 3'SL structure eliminated aldolase binding, suggesting that the binding site for this protein is located near the top of the SL. These cell proteins may play roles in regulating the functions of the genomic 3' NCR.     

Alfalfa mosaic virus temperature-sensitive mutants. II. Early functions encoded by RNAs 1 and 2

Mutants Bts 03 and Mts 04 of alfalfa mosaic virus (AIMV) have temperature-sensitive mutations in genomic RNAs 1 and 2, respectively. These mutants are defective in the production of viral minus-strand RNA, coat protein, and infectious virus when assayed in cowpea protoplasts at the nonpermissive temperature (30 degrees). To determine the temperature-sensitive step in the replication cycle, mutant-infected protoplasts were shifted from an incubation temperature of 25 degrees (permissive temperature) to 30 degrees at different times during a 24-hr incubation period. For both mutants an initial incubation of infected protoplasts for 6 hr at 25 degrees was sufficient to permit a normal minus-strand RNA synthesis, translation of RNA 4 into coat protein, and assembly of infectious virus during the subsequent incubation at the nonpermissive temperature. Probably, AIMV RNAs 1 and 2 encoded proteins are produced early in infection and the mutant proteins are protected from inactivation at 30 degrees once they are incorporated in a functional structure.     

Alfalfa mosaic virus temperature-sensitive mutants IV. Tbts 7, a coat protein mutant defective in an early function

Tbts 7 is coat protein mutant of alfalfa mosaic virus (AIMV) which replicates in tobacco leaf disks at 23° but not at 30°, whereas the wild-type (wt) replicates at both temperatures. To analyze the temperature-sensitive step in virus multiplication, the replication of Tbts 7 in protoplasts was investigated. The data indicated that poly-l-ornithine (PLO), when present in the inoculum, selectively interfered with the uncoating in cowpea protoplasts of the mutant virions containing RNA 3 (top component b, Tb) whereas uncoating of virions containing RNAs 1 and 2 was not noticably affected. When PLO in the inoculum was replaced by polyethylene glycol (PEG), Tbts 7 was able to replicate in cowpea and in tobacco protoplasts at 25° but not at 30°. At the restrictive temperature the replication of mutant RNA 3 was selectively defective. An infection induced by an inoculum containing a mixture of Tbts 7 genomic RNAs and wt coat protein was similarly temperature sensitive in RNA synthesis, indicating that a defect in uncoating of Tb is not responsible for the temperature-sensitive behavior. Addition of wild-type Tb to a Tbts 7 inoculum restored the wt phenotype. Under these conditions, at both 25 and 30°, only wt RNA 3 was replicated and not the mutant RNA 3 present in the inoculum. The results are discussed in respect of the early function of AIMV coat protein in the virus replication cycle.     

Expression of alfalfa mosaic virus and tobacco rattle virus coat protein genes in transgenic tobacco plants

Using the Agrobacterium tumefaciens binary vector system, a chimeric gene consisting of the cauliflower mosaic virus 35 S promoter, alfalfa mosaic virus (AIMV) coat protein (CP) cistron, and the nopaline synthase polyadenylation signal was integrated into the genome of Nicotiana tabacum cv. Samsun NN. In 70% of the transgenic tobacco plants the chimeric mRNA and its translation product could be detected. CP accumulated to levels up to 0.05% of the soluble leaf protein. The accumulation was independent of leaf age. The same approach was undertaken for the CP of tobacco rattle virus (TRV). The chimeric gene was integrated in the genome of Nicotiana tabacum cv. Xanthi nc. The results with respect to the accumulation of the chimeric mRNA and TRV CP in leaves of transgenic tobacco plants were comparable to those with AIMV transformed plants. Plants accumulating AIMV CP were highly resistant to infection with AIMV nucleoproteins but could be infected with a mixture of AIMV RNAs 1-4. Moreover, a mixture of AIMV RNAs 1, 2, and 3 was infectious to these plants but not to nontransformed control plants.     

Removal of the N-terminal part of alfalfa mosaic virus coat protein interferes with the specific binding to RNA 1 and genome activation

Trypsinized coat protein of alfalfa mosaic virus lacking 25 amino acids at its N terminus still has the capability to form complexes with RNA which are detectable by sedimentation in sucrose gradients. However, it does not protect specific sites on the RNA against degradation by ribonuclease, as the native coat protein does (D. Zuidema, M. F. A. Bierhuizen, B. J. C. Cornelissen, J. F. Bol, and E. M. J. Jaspars (1983) Virology 125, 361-369.). The trypsinized coat protein has lost the capacity of the native coat protein to make the genome RNAs of alfalfa mosaic virus infectious or to interfere with the infectivity brought about by the native coat protein. These findings suggest that genome activation occurs via binding of the N-terminal part of the coat protein to specific sites on the RNAs.     

Alfalfa mosaic virus temperature-sensitive mutants. I. Mutants defective in viral RNA and protein synthesis

The replication in cowpea protoplasts of temperature-sensitive (ts) mutants of alfalfa mosaic virus (AIMV) was studied at the permissive (25 degrees) and the restrictive (30 degrees) temperature. Using the Northern blot hybridization technique, it was shown that at the restrictive temperature two RNA 1 mutants, Bts 03 and Bts 04, and two RNA 2 mutants, Mts 03 and Mts 04, were all defective in the synthesis of viral minus-strand RNA, whereas the synthesis of the plus-strand genomic RNAs 1, 2, and 3 and the subgenomic coat protein messenger, RNA 4, was relatively unimpaired. In Bts 04 inoculated protoplasts the RNA 4 produced at 30 degrees was translated into coat protein and viral RNA was encapsidated to give infectious virus. RNA 4 in Bts 03 and Mts 04 infected protoplasts was not translated into coat protein at 30 and consequently there was no assembly of infectious virus. Protein synthesis by Mts 03 was not investigated. A1MV RNAs 1 and 2 encoded proteins are both involved in the synthesis of viral minus-strand RNA and the translation of RNA 4 and possibly other viral messengers. The results with Bts 03 and Bts 04 show that the two functions of the RNA 1 encoded protein can be mutated separately.     

Evidence that alfalfa mosaic virus infection starts with three RNA-protein complexes

The tripartite genome of alfalfa mosaic virus (AMV) needs to be activated by its coat protein. To establish whether coat protein exerts its role by interacting structurally with one, two, or all three AMV-RNA species, the infectivity of mixtures of RNA-protein complexes with free RNAs were studied (Smit and Jaspars, Virology 104, 454-461, 1980). These studies were not fully conclusive since some redistribution of coat protein does occur as soon as RNAs are brought into contact with RNA-protein complexes. This problem was overcome by the use of ts mutants of AMV. Free ts coat protein subunits were not able to activate the wt genomic RNAs at 30 degrees in tobacco. Once complexed to the genomic RNAs at 0 degrees , the biological activity of the ts coat protein remained when assayed at the nonpermissive temperature. Apparently, the ts coat protein is inactivated during attempted redistribution at 30 degrees . Studies of mixtures of RNA-protein complexes and free RNA show that coat protein has to be present on at least two of the three RNA species. This result in combination with previous results (Smit and Jaspars, 1980) warrants the conclusion that the alfalfa mosaic virus infection starts with three RNA-protein complexes.     

The nucleotide sequence and genome organization of the RNA2 and RNA3 segments in broad bean mottle virus.

Complete nucleotide sequences of broad bean mottle virus (BBMV) genomic RNAs 2 and 3 were determined. They consist of 2811 and 2293 nucleotides, respectively. Both RNAs are caped and, unlike in other tricornaviruses, both initiate with an A residue. BBMV RNA2 is monocistronic and encodes an 815 amino acid 2a protein, whereas RNA3 is dicistronic, encoding for a 295 amino acid 3a protein and for the 190 amino acid coat protein. A central, 423 amino acid 2a protein core region is highly homologous among the three bromoviruses, whereas both N- and C-termini are more heterologous. Most of the homologies among 3a proteins are concentrated within the N-termini two-thirds of the molecule that is predominantly hydrophobic, whereas the C-terminal one-third contains a large number of charged amino acids. The homologies among coat proteins are clustered within several mostly hydrophobic, or neutral, domains. The 5' noncoding region of the RNA2 has 110 nucleotides, whereas that of RNA3 contains 330 nucleotides. As in cowpea chlorotic mottle virus, but unlike in Brome mosaic virus, the 5' noncoding region includes subgenomic promoter-like sequences. The BBMV RNA3 intercistronic region also has subgenomic promoter sequences and contains a long poly(A) stretch. At the 3' end, BBMV RNAs 2 and 3 have 257 and 236 noncoding nucleotides, respectively.     

Role of alfalfa mosaic virus coat protein in regulation of the balance between viral plus and minus strand RNA synthesis

Replication of wild type RNA 3 of alfalfa mosaic virus (AIMV) and mutants with frameshifts in the P3 or coat protein (CP) genes was studied in protoplasts from tobacco plants transformed with DNA copies of AIMV RNAs 1 and 2. Accumulation of viral plus and minus strand RNAs was monitored with strand-specific probes. A frameshift in the P3 gene did not change the asymmetry in plus/minus strand accumulation observed for the wild type. A frameshift early in the CP gene resulted in a 100-fold reduction in plus strand accumulation and a 3- to 10-fold increase in minus strand accumulation. A frameshift late in the CP gene caused a similar reduction in plus strand accumulation but had no effect on minus strand accumulation. This latter mutant accumulated nearly wild type levels of a truncated CP molecule. Apparently, wild type AIMV CP up-regulates plus strand accumulation and down-regulates minus strand accumulation and these two functions can be mutated separately.