Molecular weights of plant viral RNAs determined by gel electrophoresis under denaturing conditions

Expression of Middle-Component RNA of Cowpea Mosaic Virus: In Vitro Generation of a Precursor to Both Capsid Proteins by a Bottom-Component RNA-Encoded Protease from Infected Cells

The expression of the middle-component (M) RNA of cowpea mosaic virus was studied by means of in vitro translation. In both the wheat germ extract and the rabbit reticulocyte lysate, M RNA was translated into two overlapping polypeptides of 95 and 105 kilodaltons. Incubation of these polypeptides with 30,000 x g supernatant fractions from cowpea mesophyll protoplasts inoculated with complete virus or with separate bottom (B) components alone resulted in extensive processing, yielding polypeptides of 60, 58, 48, and 47 kilodaltons. Similar proteolytic activity was found associated with the in vitro translation products from the bottom-component RNA, demonstrating that the protease present in infected cells is encoded by B RNA. Using antisera raised against the separate capsid proteins VP23 and VP37, it was shown that the 60-kilodalton cleavage product is the precursor to both capsid proteins. Cleavage of nascent 95- and 105- kilodalton polypeptides by the in vivo protease demonstrated that this capsid protein precursor is located C terminally within both polypeptides and that the synthesis of these two overlapping polypeptides is the result of two initiation sites on middle-component RNA. In addition, a second virus-induced proteolytic activity, capable of releasing VP23 from the 95- and 105-kilodalton polypeptides, was detected in leaves of infected plants, but not in infected mesophyll protoplasts. A model for the expression of the middle-component RNA is presented.

Characterization of the 3' Termini of the RNAs of Cowpea Mosaic Virus

A sequence of polyadenylic acid, homogeneous in composition but heterogeneous in length, was isolated from complete pancreatic RNase digests of both middle and bottom RNAs of cowpea mosaic virus. The polyadenylic acid was 3'-terminal and occurred once per molecule. A fragment consisting of the polyadenylic acid and approximately the next 25 nucleotides could be isolated from complete T1 RNase digests of either RNA. The region adjacent to the polyadenylic acid in both RNAs was rich in pyrimidines. The mobilities of the fragments in 12.4% polyacrylamide-8 M urea gels were used to estimate their lengths and to calculate number average and weight average molecular weights.

Evidence That the 32,000-Dalton Protein Encoded by Bottom-Component RNA of Cowpea Mosaic Virus is a Proteolytic Processing Enzyme

Translation of middle-component RNA of cowpea mosaic virus in vitro produced two polypeptides of 95 and 105 kilodaltons (95K and 105K, respectively) with overlapping amino acid sequences, which were specifically cleaved by a protease encoded by the bottom-component RNA. The proteolytic cleavage was studied by the addition of antibodies raised against various bottom-component RNA-encoded proteins to extracts prepared from bottom-component RNA-inoculated cowpea protoplasts. Since antiserum to the 32K polypeptide efficiently inhibited the proteolytic activity of such extracts, although antiserum to VPg or to the 170K polypeptide did not, evidence was obtained which indicates that the 32K polypeptide represents the protease involved. Fractionation of proteolytically active extract by glycerol gradient centrifugation demonstrated that 32K polypeptides do not exist as free proteins but are aggregated to the bottom-component RNA-encoded 170K, 84K, 60K, or 58K polypeptides. Maximal proteolytic activity was observed for 32K polypeptides associated with 170K polypeptides, suggesting that the activity was unstable and confined to newly synthesized molecules.

In Vitro Replication of Cowpea Mosaic Virus RNA III. Template Recognition by Cowpea Mosaic Virus RNA Replicase

Cowpea mosaic virus (CPMV) RNA replicase has been purified about 200-fold from CPMV-infected Vigna unguiculata leaves. Optimal reaction conditions for replicase activity have been established that allow RNA synthesis to proceed for at least 15 h. Using a polymerase assay under conditions optimal for CPMV RNA-directed RNA synthesis, all natural RNA species tested appeared to be able to direct the incorporation of labeled ribonucleotides, whereas synthetic homoribopolymers were either inactive or only slightly active. Using a nitrocellulose membrane filter assay to measure complex formation between the replicase preparation and various RNA species, all natural RNA species tested, except that of the comovirus radish mosaic virus, appeared to be unable to compete with (32)P-labeled CPMV RNA in binding to replicase. We propose that CPMV replicase is actually template specific but does not display this property in a polymerase assay, since labile complexes between heterologous templates and replicase become stabilized by the formation of phosphodiester bonds. From homoribopolymer competition binding experiments we conclude that the polyadenylic acid on the CPMV genome might be a part of the replicase binding site.

Inhibition of proteolytic processing of the polyproteins of cowpea mosaic virus by hemin

Cleavages of the polyproteins synthesized from cowpea mosaic virus (CPMV) B RNA and M RNA in rabbit reticulocyte lysates are inhibited by hemin. Cleavage of the CPMV B RNA-encoded 200K polyprotein and of the M RNA-encoded 60K intermediary precursor protein were most sensitive to hemin inhibition, while cleavages of other precursor proteins were less sensitive. A significant observation was that at a hemin concentration of 25 microM, but not at higher concentrations, the 60K protein was cleaved to yield the two viral capsid proteins. This cleavage reaction has not been observed in vitro previously.

Orientation of the Cleavage Map of the 200-Kilodalton Polypeptide Encoded by the Bottom-Component RNA of Cowpea Mosaic Virus

The genomic organization of the bottom-component RNA of cowpea mosaic virus was studied. In vivo, this RNA encodes at least eight different polypeptides of 170, 110, 87, 84, 60, 58, 32, and 4 kilodaltons (K), the last polypeptide representing the genome-bound protein VPg. In rabbit reticulocyte lysates, bottom-component RNA is translated into a 200K polypeptide which is then processed to give the 32 and 170K polypeptides also found in vivo. By pulse-labeling the 200K primary translation product, we now show that the 32 and 170K polypeptides are derived from the NH 2 -terminal and COOH-terminal parts of this polypeptide, respectively. Comparison of the proteolytic peptide patterns of 170K polypeptides synthesized in vitro and pulse-labeled at either the NH 2 -terminal or the COOH-terminal end with the patterns of the 170 and 110K polypeptides found in vivo demonstrates that the order within the 200K primary translation product of cowpea mosaic virus bottom-component RNA is as follows: NH 2 -32K polypeptide-58K polypeptide-VPg-24K polypeptide-87K polypeptide-COOH.

Cowpea Mosaic Virus-Encoded Protease Does Not Recognize Primary Translation Products of M RNAs from Other Comoviruses

The protease encoded by the large (B) RNA segment of cowpea mosaic virus was tested for its ability to recognize the in vitro translation products of the small (M) RNA segment from the comoviruses squash mosaic virus, red clover mottle virus, and cowpea severe mosaic virus (CPsMV, strains Dg and Ark), and from the nepovirus tomato black ring virus. Like M RNA from cowpea mosaic virus, the M RNAs from squash mosaic virus, red clover mottle virus, CPsMV-Dg, and CPsMV-Ark were all translated into two large polypeptides with apparent molecular weights which were different for each virus and even for the two CPsMV strains. Neither the in vitro products from squash mosaic virus, red clover mottle virus, and CPsMV M RNAs nor the in vitro product from tomato black ring virus RNA-2 were processed by the cowpea mosaic virus-encoded protease, indicating that the activity of this enzyme is highly specific.

The location of the first AUG codons in cowpea mosaic virus RNAs

We have made use of the known sequence of the 5' ends of both CPMV RNAs to synthesise an oligodeoxynucleotide which can prime second-strand DNA synthesis on full-length cDNA copies of both RNAs. By priming synthesis in the presence of dideoxynucleoside triphosphates, we have determined the positions of the first AUG codons in each RNA. These occur at positions 115 and 207 on M and B RNA respectively. By using a cloned double-stranded DNA fragment derived from near the 5' end of M RNA as a primer additional sequence from the 5' terminal region of M RNA has been obtained.

Terminal uridylyl transferase of Vigna unguiculata: purification and characterization of an enzyme catalyzing the addition of a single UMP residue to the 3'-end of an RNA primer

An enzyme which catalyzes the addition of a single UMP residue from UTP to the 3'-end of an RNA primer and which is referred to as terminal uridylyl transferase (TUT) has been extensively purified from the membrane fraction of vigna unguiculata leaves. The purification procedure involved (i) solubilization by cation depletion (ii) DEAE-Sepharose CL-6B column chromatography (iii) affinity chromatography of poly(U)-Sepharose 4B and (iv) glycerol gradient centrifugation. The molecular weight of the native enzyme was approximately 50,000 as determined by velocity sedimentation. Under conditions that were optimal for UMP-incorporation (5 mM Mg2+, low salt, 30 degrees C) TUT displayed a marked specificity for UTP as substrate, was unable to incorporate deoxyribonucleoside triphosphates and required a single-stranded oligo- or polyribonucleotide as primer. When oligoA20, tRNAasp of E. coli or alfalfa mosaic virus RNA 4 were used as primers at various substrate to primer ratio's, the vast majority of the product appeared to consist of primer molecules elongated with a single UMP residue as shown by polyacrylamide gelelectrophoresis and nearest neighbour analysis. We believe TUT to be a novel enzyme which has not been reported before and which may be a feasible tool in RNA sequencing as it enables the specific 3'-terminal labeling of RNA molecules.

Expression of Bottom Component RNA of Cowpea Mosaic Virus in Cowpea Protoplasts

Upon inoculation of cowpea protoplasts with the bottom component of cowpea mosaic virus, at least six virus-induced proteins (with sizes of 170, 110, 87, 84, 60, and 32 kilodaltons) are synthesized, but not the capsid proteins (37 and 23 kilodaltons). These bottom-component-induced proteins were studied with respect to their genetic origin and mode of synthesis. The analyses were based on their electrophoretic peptide patterns resulting from partial digestion with Staphylococcus aureus protease V8. Comparison of the peptide patterns of the virus-induced proteins with those of the cowpea mosaic virus RNA-coded polypeptides produced in rabbit reticulocyte lysate showed that the 170- and 32-kilodalton polypeptides, which are the first viral products in cowpea mosaic virus-infected cells, were actually coded by the bottom component RNA of the virus. The 110-, 87-, and 84-kilodalton polypeptides, and possibly the 60-kilodalton polypeptide, appeared to have amino acid sequences in common with the 170-kilodalton polypeptide, demonstrating that they were virus coded as well. The results indicated that cowpea mosaic virus bottom component RNA was translated in vivo into a single 200-kilodalton polyprotein from which probably all bottom-component-specific proteins arose by three successive cleavages.

Alfalfa mosaic virus RNA. Determination of the sequence homology between the four RNA species and a comparison with the four RNA species of cucumber mosaic virus

The method of Taylor et al. [Taylor, J. M., Illmensee, R & Summers, J. (1976) Biochim. Biophys. Acta, 442, 324--330 and Gould and Symons (1977) Nucleic Acids Res. 4, 3787--3802] has been used to transcribe complementary DNA probes from the four major RNAs of alfalfa mosaic virus (AMV). Analysis of the kinetics of hybridization of these probes in homologous and heterologous complementary DNA . RNA hybridization reactions has shown that the sequence of the smallest RNA (RNA 4), which contains the coat protein gene, is present within RNA 3 and located at the 3' end of this RNA species. RNAs 1 and 2 are unique RNA molecules with little or no sequence homology between them or RNAs 3 and 4. This latter observation contrasts with the situation that occurs in cucumber mosaic virus (CMV) as CMV RNAs 1--4 were shown to have a common nucleotide stretch of 200 bases at their 3' termini; the location of RNA 4 within RNA 3 of CMV was also shown to be at the 3' end of this RNA species.

Introduction of hidden breaks during rRNA maturation and ageing in Tetrahymena pyriformis

The stability of Tetrahymena pyriformis cytoplasmic rRNAs and nuclear rRNA precursors has been studied by polyacrylamide gel electrophoresis under partly and completely denaturing conditions. Cytoplasmic 17-S rRNA (Mr = 0.66 X 10(6) consists of a continuous polynucleotide chain throughout its lifetime, whereas the bulk of 26-S rRNA (Mr = 1.2m X 10(6) dissociates upon denaturation. Two large fragments (F1, F2) of somewhat different molecular weights (Mr 0.63 X 10(6) and 0.58 X 10(6) and the small 5.8-S rRNA fragment (Mr about 50 000) are regularly observed. Some additional distinct minor fragments (F3-F6) are noted under certain preparative conditions, suggestive of artifactual origin. The following conclusions were made from the data obtained . (a) Newly synthesized 26-S rRNA molecules do not contain the 'central' hidden break (separating F1 and F2) until about 15 min after their appearance in the cytoplasm; however, they release during denaturation the 5.8-S and/or a short-lived 7-S fragment (Mr about 75 000) which might represent a direct precursor to the 5.8-S rRNA. (b) The immediate nuclear precursor to the 26-S rRNA (Mr 1.39 X 10(6) releases a small fragment of similar size (7 S). (c) The largest stable transcription product of the rDNA (pre-rRNA) does not contain any hidden break.

Cowpea mosaic virus RNAs have neither m7GpppN ... nor mono-, di- or triphosphates at their 5' ends

32P-labeled cowpea mosaic virus (CPMV) RNAs were analyzed for their 5' termini by three different fingerprinting standard procedures. These analyses showed unequivocally that CPMV RNAs lack a structure like m7GpppN ... at their 5' termini. In addition, neither mono-, di- or triphosphorylated [(p)(p)pN ....] termini were found in the respective fingerprints. The inability to label the 5' termini treatment with gamma-32P-ATP and polynucleotide kinase, either per se or after pretreatment with alkaline phosphatase, strongly suggests the absence of a free 5'-OH and a free 5'-phosphate at the 5' terminal nucleotide in CPMV RNAs. The various analyses also showed that no 2' -O-methylated nucleotides, N6-methyladenosines or pseudo-uridines are present in CPMV RNAs.

Lengths and patterns of transcriptional units in the amplified nucleoli of oocytes of Xenopus laevis

Transcriptionally active chromatin from peripheral amplified nucleoli of lampbrush-chromosome stage oocytes of Xenopus laevis was dispersed and spread in various solutions of low salt concentrations (including some with additions of detergents) and examined by electron microscopy. Nucleolar material from oocytes of animals with normal (2-nu) and mutant (1-nu) genetical constitution of nucleolus organizers was compared. Histograms showing the distributions of the length of matrix units, apparent spacer intercepts, and the total repeating units of the rDNA containing chromatin axes revealed a significant degree of heterogeity, with indications of subclasses and predominant repeat unit size classes of 3.3 amd 3.8 micron length. The correspondence of matrix unit length to the molecular weight of the first stable product of rDNA transcription was studied using gel electrophoresis of labelled pre-rRNA under non-denaturing and denaturing conditions. Evaluations of individual strands of nucleolar chromatin further demonstrated the existence of both (i) strands with obviously homogeneous repeating units of and (ii) strands with intra-axial heterogeneity of rDNA subunits. "Prelude complexes", i.e. groups of transcriptional complexes in apparent spacer intercepts, were not infrequently noted. The data are compared with the measurements of lengths of repeating units in fragments of rDNA obtained by digestion with EcoRI endonuclease as described by Morrow et al.(1974) and Wellauer et al. (1974,1976a, b). The results are discussed in relation to problems of variations in the modes of arrangement of the pre-rRNA genes, the state of packing of rDNA during transcription, and possible mechanisms of the amplification process.

An efficient mRNA-dependent translation system from reticulocyte lysates

A simple method is described for converting a standard rabbit reticulocyte cell-free extract (lysate) into an mRNA-dependent protein synthesis system. The lysate is preincubated with CaCl2 and micrococcal nuclease, and then excess ethyleneglycol-bis(2-aminoethylether)-N,N'-tetraacetic acid is added to chelate the Ca2+ and inactivate the nuclease. Lysates treated in this way have neglibible endogenous amino acid incorporation activity, but 75% of the activity of the original lysate can be recovered by the addition of globin mRNA. The efficiency of utilisation of added mRNA and the sensitivity of the system are both very high. No residual nuclease activity could be detected, and the tRNA is functionally unimpaired. Several different species of mRNA have been shown to be translated efficiently into full-sized products of the expected molecular weight up to about 200000, and there is no detectable accumulation of incomplete protein products. The efficient translation of RNA from two plant viruses (tobacco mosaic virus and cowpea mosaic virus) required heterologous tRNA.

The molecular weights of yeast ribosomal precursor RNAs

The molecular weights of the predominant rRNA precursors as well as those of 26-S and 17-S mature rRNA from Saccharomyces carlsbergensis were determined by polyacrylamide gel electrophoresis in the presence of formamide. Mature 26-S + 5.8-S rRNA was found to have a molecular weight of 1.24 X 10(6) while their immediate precursor, 29-S RNA, had a molecular weight of 1.52 X 10(6). Values of 0.70 X 10(6) and 0.82 X 10(6) were obtained for the molecular weights of mature 17-S rRNA and its 18-S precursor. Finally the 37-S precursor, common to both 29-S and 18-S RNA, was found to have a molecular weight of 2.80 X 10(6). Each precursor rRNA, therefore, contains extra sequences not found at the next stage of maturation.

The effect of double-stranded cowpea mosaic viral RNA on protein synthesis

The effect of double-stranded cowpea mosaic viral RNA on several in vitro protein synthesizing systems was studied. No inhibitory effect of this RNA at concentrations up to 16 mug/ml was found in wheat germ protein synthesis programmed with cowpea mosaic viral-, alfalfa mosaic viral- or globin 9 S-RNA. At high concentrations of this double-stranded RNA, inhibition of Escherichia coli in vitro protein synthesis programmed with MS-2- and cowpea mosaic viral-RNA was found, whereas at low concentrations its inhibitory effect on rabbit reticulocyte in vitro protein synthesis was strong. The implications of these observations for the suggestions of other authors, based on the study of mammalian protein synthesizing systems, are discussed.

Molecular weights of maize mitochondrial and cytoplasmic ribosomal RNAs under denaturing conditions

The molecular weights of maize cytoplasmic and mitochondrial rRNAs were determined by gel acrylamide electrophoresis under non-denaturing and denaturing conditions. The molecular weights of mitochondrial rRNAs (0.76-10-6 and 1.25-10-6) exceeded those of cytoplasmic rRNAs (0.67-10-6 and 1.19-10-6) when electrophoresed in 8 M urea at 60 degrees C. Electrophoresis in 1.1 M formaldehyde resulted in similar values except for heavy mitochondrial rRNA, which exhibited a higher molecular weight than observed in 8 M urea. The observed values for cytoplasmic rRNAs, especially the heavy component, represent a decrease from estimates obtained under non-denaturing conditions. This is the first report of the electrophoretic examination of higher plant rRNAs under denaturing conditions.