Genome-linked Protein Research Articles

Evidence that Potato Leafroll Virus RNA is Positive-stranded, is Linked to a Small Protein and Does Not Contain Polyadenylate

SUMMARY RNA extracted from particles of potato leafroll virus (PLRV) infected tobacco mesophyll protoplasts. Treating the RNA with proteinase K did not abolish its infectivity. In messenger-dependent rabbit reticulocyte lysate, PLRV RNA induced the synthesis of specific polypeptides: a major product of mol. wt. 71000 but no product the size of coat protein. PLRV RNA is therefore positive-stranded. A genome-linked protein (apparent mol. wt. 7000) was detected in preparations of PLRV RNA but no polyadenylate sequence was found. These features may prove to be characteristic of luteoviruses.

Antibodies Against the Genome-Linked Protein VPg of Cowpea Mosaic Virus Recognize a 60,000-Dalton Precursor Polypeptide

We have prepared a rabbit antiserum specifically directed against the genome-linked protein (VPg) of cowpea mosaic virus by injecting an hydrolysate of purified virion RNA. Using this antiserum as a probe in combination with "Western" (protein) blots of subcellular fractions of cowpea mosaic virus-infected cowpea (Vigna unguiculata) cells, we have detected a bottom component RNA-encoded, 60,000-dalton polypeptide which is membrane bound and presumably represents the immediate precursor of VPg.

Specificity and Properties of the Genome-linked Proteins of Nepoviruses

SUMMARY The infectivity of the RNA of six nepoviruses was decreased or abolished by proteinase K treatment, whereas that of the RNA of cowpea mosaic virus (comovirus group) or tomato bushy stunt virus was unaffected. The extent of the decrease in infectivity was characteristic for each nepovirus and was independent of the plant species used as virus source or as assay host. The infectivity of raspberry ringspot virus (RRV) RNA was less affected than that of the other nepoviruses but treatment with Pronase decreased infectivity more than treatment with proteinase K. Proteinase K treatment also abolished the infectivity for tobacco mesophyll protoplasts of RNA of tobacco ringspot virus (TRSV) and tomato black ring virus (TBRV). Tests on virus RNA, labelled with 125I by the chloramine T method, provided evidence that three nepoviruses and Echtes Ackerbohnenmosaik-Virus (EAMV; comovirus group) have genome-linked proteins (VPg). Pronase treatment rendered about half (RNA of strawberry latent ringspot virus; SLRV), or nearly all (RNA of the other nepoviruses and EAMV), of the 125I soluble in 70% ethanol. Treatment of nepovirus RNA with ribonuclease P1 yielded a product with an estimated mol. wt. of 4000 ± 900. Mobilities in polyacrylamide gels of VPg from the RNA of different viruses differed slightly (SLRV > TBRV > TRSV > RRV). TRSV VPg yielded one 125I-labelled tryptic peptide whereas the genome-linked proteins of RRV and TBRV both yielded two major products, of which one was resistant to further digestion and the other was converted, apparently via intermediates, to a second more stable product. No difference was detected between the tryptic peptides obtained from VPg of different strains of RRV, or of TBRV, or between those obtained from RNA-1, RNA-2 or RNA-3 (satellite RNA) of TBRV. Nepovirus VPg is therefore virus-specific. It seems to be coded on RNA-1 and probably has multiple functions.

Antibodies against the chemically synthesized genome-linked protein of poliovirus react with native virus-specific proteins

The genome-linked protein (VPg) of poliovirus has been chemically synthesized, coupled to bovine serum albumin carrier and injected into rabbits. An antibody response was elicited not only by the full-length synthetic VPg peptide, but also by a synthetic 14-amino-acid carboxy-terminal peptide. All antisera reacted with virus-specific proteins from HeLa cells infected with poliovirus. Three of these proteins have previously been implicated by others as precursors of VPg. No free cytoplasmic VPg could be detected, and the antibodies did not react with radiolabeled proteins from uninfected cells.

Genome-linked proteins of viruses

Genome-linked proteins of viruses

Comparative sequence analysis of the 5′-terminal noncoding regions of poliovirus vaccine strain sabin 1, Sabin 2, and Sabin 3 genomes

Complementary DNAs (cDNAs) were synthesized with virion RNAS from immunologically distinct vaccine strains of poliovirus, that is, Sabin 1 (LSc, 2ab), Sabin 2 (p712, Ch, 2ab), and Sabin 3 (Leon 12a 1b). Restriction endonuclease HaeIII cleavage patterns of these cDNAs suggested striking difference in RNA sequences among these poliovirus serotypes. The virion RNA of Sabin 3 was shown to have a genome-linked protein (VPg) and physical properties of the VPg were identical to those of VPgs of the other poliovirus strains. Virion RNA from each serotype was labeled with 125I-Bolton-Hunter reagent, after proteinase K treatment to remove all but a small peptide of the VPg which covalently linked to the 5′ terminus. The specifically 5′-end-labeled RNAs were analyzed by rapid RNA sequencing techniques. Sequences of the first 20 nucleotides were identical in Sabin 1, Sabin 2, and Sabin 3 strains, that is, VPg-pU-U-A-A-A-A-C-A-G-C-U-C-U-G-GG-G-U-U-G. Complete sequence homology was observed between virion RNAs of Sabin 1 and Sabin 2 strains up to the 43rd nucleotide from the 5′ end except for the 25th nucleotide by a “wandering spot” analysis of 125I-labeled RNA mixture of these two strains. These results suggested that serotypes of poliovirus were derived by numerous mutations from a putative prototype poliovirus, and that the homologous sequence at 5′ termini, conserved through a long evolutional process, may have essential roles for replication and viral function of poliovirus.

Removal of the genome-linked protein of foot-and-mouth disease virus by rabbit reticulocyte lysate.

Rabbit reticulocyte lysate cleaves the genome-linked protein VPg from foot-and-mouth disease virus (FMDV) RNA. This activity could be reliably monitored since removal of the protein resulted in a change in migration in polyacrylamide gels of the small specific 5' and fragment of the RNA (S fragment). The unlinking activity cleaved the bond between the tyrosine residue of VPg and the RNA to leave a 5' phosphate on the RNA. The 5' sequence of the RNA from which VPg had been removed by rabbit reticulocyte lysate was the same as that of FMDV mRNA isolated from infected cells. VPg released from the RNA was rapidly degraded by the rabbit reticulocyte lysate to material which eluted with the inclusion volume of a Sepharose 6B column and partitioned to the aqueous phase during phenol extraction. The unlinking activity was inhibited by heating the lysate to 56 degrees C, by sodium dodecyl sulfate (SDS), EDTA, and Zn2+ ions but was unaffected by reducing agents, a translation inhibitor, and a number of protease and RNase inhibitors.

The RNA of Tobacco etch virus: Further characterization and detection of protein linked to RNA

TEV-RNA was separated into poly(A) + and poly(A) − RNA by affinity chromatography. Both classes of RNA have similar base ratios. The poly(A) segment in the RNA was shown to be located at the 3′-OH end by dihydroxyborylaminoethyl-cellulose chromatography. Although the poly(A) was heterodisperse in length, ranging from about 200 to less than 33 AMP residues, two size classes averaging about 150 and 30 AMP residues, respectively, could be recognized. The presence of a genome-linked protein of molecular weight 6000 daltons was detected. The viral RNA is infectious even after proteinase K treatment, indicating that the genome-linked protein is not required for infectivity.

Poliovirus replication proteins: RNA sequence encoding P3-1b and the sites of proteolytic processing.

A partial amino-terminal amino acid sequence of each of the major proteins encoded by the replicase region (P3) of the poliovirus genome has been determined. A comparison of this sequence information with the amino acid sequence predicted from the RNA sequence that has been determined for the 3' region of the poliovirus genome has allowed us to locate precisely the proteolytic cleavage sites at which the initial polyprotein is processed to create the poliovirus products P3-1b (NCVP1b), P3-2 (NCVP2), P3-4b (NCVP4b), and P3-7c (NCVP7c). For each of these products, as well as for the small genome-linked protein VPg, proteolytic cleavage occurs between a glutamine and a glycine residue to create the amino terminus of each protein. This result suggests that a single proteinase may be responsible for all of these cleavages. The sequence data also allow the precise positioning of the genome-linked protein VPg within the precursor P3-1b just proximal to the amino terminus of polypeptide P3-2.

Replication of RNA-1 of Tomato Black Ring Virus Independently of RNA-2

SUMMARY In hybridization experiments, using complementary DNA (cDNA) copies of the two genome parts of tomato black ring virus (TBRV RNA-1 and RNA-2), no sequence homology between the two RNA species was detected. When tobacco mesophyll protoplasts were inoculated with purified middle component particles, which contain only RNA-2, no replication of TBRV RNA could be detected. However, when they were inoculated with purified bottom component particles, which contain only RNA-1, extracts made 24 or 48 h later contained RNA that had the same mobility as RNA-1 in polyacrylamide-agarose gels, and that hybridized to cDNA copies of RNA-1. Thus RNA-1 can replicate in protoplasts that do not contain RNA-2. Moreover, this RNA-1 was capable, when mixed with nucleoprotein particles containing RNA-2, of inducing the formation of local lesions in Chenopodium amaranticolor leaves, and therefore was intact and attached to the genome-linked protein. The genome-linked protein of nepoviruses is probably virus-coded, and its production in protoplasts inoculated with bottom component particles therefore suggests that RNA-1 contains the gene for this protein.

The genome-linked protein of cowpea mosaic virus is coded by RNA from the bottom component

It has recently been shown that RNA from the bottom component of cowpea mosaic virus is capable of self-replication in cowpea mesophyll protoplasts, providing a tool for the investigation of the contribution of each RNA strand toward viral multiplication. Evidence is presented here, using this system, to show that the genome-linked protein is coded by the RNA from the bottom component. As the replicase function is coded by this RNA, the results remain consistent with the involvement of the genome-linked protein in viral RNA replication.

The genome-linked protein of picornaviruses. VII. Genetic mapping of poliovirus VPg by protein and RNA sequence studies

The poliovirus genome-linked protein (VPg) has been subjected to radiochemical microsequence analysis. Sequence studies of virion RNA by a modification of Sanger's dideoxy method have revealed a base sequence corresponding to the amino acid analysis. This result proves that VPg is virus-encoded. The RNA sequence has allowed us to predict the total amino acid sequence of VPg and part of its precursor. VPg is, at most, 27 amino acids long. It maps within the 3′ terminal segment of the viral genome that encodes the precursor polypeptide NCVP1b for the virus-specific RNA polymerase NCVP4.

Heterogeneity of the genome-linked protein of foot-and-mouth disease virus.

The genome-linked protein of foot-and-mouth disease virus was examined by electrofocusing in polyacrylamide gels. Two proteins of different charge and amino acid composition were found. The tryptic peptide maps of the proteins were dissimilar. The possible relationship between the two proteins is discussed.

Sequence of picornavirus RNAs containing a radioiodinated 5'-linked peptide reveals a conserved 5' sequence.

Virion RNA (vRNA) from poliovirus type 1 (PV1), poliovirus type 2 (PV2), and coxsackie virus B1 (Cox B1) were treated with proteinase K to remove all but a small peptide of the covalently attached 5' genome-linked virion protein (VPg). The peptide on these RNA molecules was then treated with Bolton-Hunter 125I reagent, which iodinates primary amine groups, in order to obtain specific 5'-terminal radioactive labeling. Sequences of 125I-labeled vRNAs were determined by using a set of base-specific RNases and a partial alkaline hydrolysis "ladder." The first 20 positions of these RNAs show a remarkable conservation of sequence. The initial 10 nucleotides are identical in PV1, PV2, and Cox B1, with the sequence VPg-pU-U-A-A-A-A-C-A-G-C. The next 10 nucleotides show a one-base difference between PV1 and PV2 and 50% homology between PV1 and Cox B1. This conserved 5' region may provide a recognition site for interaction between the viral mRNA and the host translation system.

The genome-linked protein of picornaviruses. VI. The 5'-terminal protein of poliovirus type 2RNA is covalently linked to a nonanucleotide identical to that of poliovirus type 1 RNA.

Digestion of poliovirus type 2[32P]-RNA with enzymes and analysis of the products by column chromatography and paper electrophoresis provides evidence that the RNA is covalently linked to a small, basic protein, VPg, via a 5'-terminal pU residue. Digestion of the RNA with proteinase K followed by labeling of the peptidyl-RNA with the Bolton and Hunter reagent [iodinated 3-(4-hydroxyphenyl)propionic acid N-hydroxysuccinimide ester] yields 5'-labeled material suitable for rapid sequencing. The 5'-terminal sequence of poliovirion type 2 RNA was determined to be VPg-pUUAAAACAG... which is identical to the sequence at the 5'-terminus of the poliovirus type 1 genome.

O4-(5'-uridylyl)tyrosine is the bond between the genome-linked protein and the RNA of poliovirus.

Virion RNA of poliovirus type 1 has been analyzed for the linkage between genome-protein VPg and the polyribonucleotide chain. Hydrolysis of the linkage with acid or alkali and enzymatic degradation lead to the conclusion that the bond is neither a phosphodiester such as nucleotidyl-(P-O)-serine (or threonine) nor a phosphoramidate such as nucleotidyl-(P-N)-amino acid. VPg-RNA can be iodinated by the Bolton and Hunter reagent [iodinated 3-(4-hydroxyphenyl)propionic acid N-hydroxysuccinimide ester] but not by the chloramine-T or lactoperoxidase procedures, an observation suggesting that VPg does not contain accessible tyrosine. However, VPg can be labeled with [3H]tyrosine in vivo. Hydrolysis of VPg-[32P]pUp with 5.6 M HCl at 110 degrees yielded 32P-labeled O4-(3'-phospho-5'-uridylyl)tyrosine that could be cleaved with micrococcal nuclease to O4-[32P]phosphotyrosine and uridine 3'-[32P]phosphate. These data establish that VPg is linked to the poliovirus genome by a bond between the O4 of tyrosine and the 5'-P atom of the terminal uridylic acid residue. The 5' end of polio genome RNA can now be described as VPg(Tyr-O)-pU-U-A-A-A-A-C-A-G.

Genome-linked protein associated with the 5' termini of bacteriophage phi29 DNA.

A DNA-protein complex was isolated from Bacillus subtilis bacteriophage phi29 by sucrose gradient sedimentation or gel filtration in the presence of agents known to break noncovalent bonds. A 28,000-dalton protein was released from this complex by subsequent hydrolysis of the DNA. The DNA-protein complex was examined for its susceptibility to enzymes which act upon the 5' and 3' termini of DNA molecules. It was susceptible to exonucleolytic degradation from the 3' termini by exonuclease III but not from the 5' termini by lambda exonuclease. Attempts to label radioactively the 5' termini by phosphorylation with T4 polynucleotide kinase were unsuccessful despite prior treatment with alkaline phosphatase or phosphatase treatment of denatured DNA. Removal of the majority of the bound protein by proteolytic digestion did not increase susceptibility. These results suggest that the linked protein is covalently attached to the 5' termini of phi29 DNA.

The genome-linked protein of picornaviruses IV. Difference in the VPg's of encephalomyocarditis virus and poliovirus as evidence that the genome-linked proteins are virus-coded

A protein (EMC-VPg) covalently attached to EMC RNA has been found whose properties are distinct from those of the genome-linked protein of poliovirus (polio-VPg). EMC-VPg isolated from virus grown in HeLa cells is identical to EMC-VPg from virus grown in L cells, as determined by urea sodium dodecyl sulfate (SDS)/polyacrylamide gel electrophoresis. In contrast, polio-VPg isolated from virus grown in HeLa cells migrates more rapidly in these gels indicating a lower apparent molecular weight. These data show that the physical properties of the genome-linked proteins of two picornaviruses depend upon the nature of the viral genome rather than what proteins are available in the host cells. The most straightforward explanation for this phenomenon is that VPg is virus-coded. Evidence is presented which suggests that, as in poliovirus, VPg is attached to the EMC genome at the 5′ terminus via the nucleotide pUp.

The 5'-terminal structures of poliovirion RNA and poliovirus mRNA differ only in the genome-linked protein VPg.

The 5'-terminal, RNase T1-resistant oligonucleotide of poliovirus mRNA has been isolated. Its sequence is pU-U-A-A-A-A-C-A-Gp, which is identical to that of virion RNA except that the genome-linked protein VPg is absent [Nomoto, A., Detjen, B., Pozzatti, R. & Wimmer, E. (1977) Nature 268, 208-213]. Because all newly synthesized viral RNAs are VPg-linked, we propose that VPg is cleaved from progeny RNA at the linkage between protein and nucleic acid prior to polyribosome formation. This may represent a new mode of processing of viral macromolecules. Virion RNA from which VPg has been cleaved proteolytically retains its specific infectivity, an observation suggesting that VPg is not involved in early steps (penetration and translation) of the infectious cycle initiated by RNA.