Separation of the complementary strands of double-stranded cucumber mosaic virus-associated RNA 5 and peanut stunt virus-associated RNA 5

The double-stranded forms of CARNA 5 and PARNA 5, viral satellites of the cucumovirus group, after denaturation and polyacrylamide gel electrophoresis under appropriate conditions allow their complementary strands to be separated and fractionated. These fractionated (+) and (-) strands are free of contaminating viral RNA fragments. They serve as templates for the preparation of cDNAs of opposite polarity, which are used to probe the viral RNA-dependent replication of CARNA 5 and PARNA 5.

Sequence homology between potato spindle tuber viroid and U3B snRNA

Sequence homology was found by computer analysis between potato spindle tuber viroid (PSTV) RNA and U3B snRNA of Novikoff hepatoma cells. This homology is colinear in arrangement, extends in length to 81% of the entire U3B snRNA molecule and is involved in the PSTV molecule unique sites which, if depicted in terms of the secondary structure of the circular PSTV molecule, reveal a conspicuous regularity in their location. A strong relation in primary structure between PSTV and U3B snRNA is demonstrated by statistical analysis.

Fractionation with ethanol of nucleic acids from viroid-infected plants

A combination of high salt and low ethanol concentration allowed the fractionation of nucleic acids extracted from viroid-infected leaves. By adding 0.4-0.5 vol of ethanol to 1 vol of a solution in 2 M LiCl of nucleic acids (containing mainly DNA, 4S, 5S, 7S, and viroid RNAs), 85% of the DNA and 75% of the 4S RNA remained in solution, from where they could be recovered by increasing the ethanol concentration, whereas almost all 5S, 7S, and viroid RNAs precipitated. When this process was repeated three times a 95% elimination of the initial DNA and 4S RNA was achieved. The method can be of special interest in viroid purification considering that DNA and 4S RNA are the most abundant contaminants in the starting solution of nucleic acids. It is suggested that the highly ordered secondary structure of viroid RNA may be responsible for its particular behavior in the ethanol fractionation of nucleic acids.

Construction of infectious potato spindle tuber viroid cDNA clones

Contiguous restriction fragments from two cloned partial-length potato spindle tuber viroid (PSTV) cDNAs were used to construct recombinant DNAs containing full-length monomeric and dimeric PSTV cDNA. When five different PSTV cDNA plasmids and RNA isolated from E. coli cells harboring these plasmids were tested for infectivity on tomato, plasmid DNAs containing PSTV cDNA dimers were infectious. RNA transcripts containing the sequence of PSTV from these plasmids were also infectious. The sequences of the viroid progeny and the cloned DNA were identical. In vitro mutagenesis of infectious PSTV cDNAs will allow systematic investigation of the role of specific sequences in viroid replication and pathogenesis.

Hop stunt viroid: molecular cloning and nucleotide sequence of the complete cDNA copy

The complete cDNA of hop stunt viroid (HSV) has been cloned by the method of Okayama and Berg (Mol.Cell.Biol.2,161-170. (1982] and the complete nucleotide sequence has been established. The covalently closed circular single-stranded HSV RNA consists of 297 nucleotides. The secondary structure predicted for HSV contains 67% of its residues base-paired. The native HSV can possess an extended rod-like structure characteristic of viroids previously established. The central region of the native HSV has a similar structure to the conserved region found in all viroids sequenced so far except for avocado sunblotch viroid. The sequence homologous to the 5'-end of U1a RNA is also found in the sequence of HSV but not in the central conserved region.

Oligomeric forms of potato spindle tuber viroid (PSTV) and of its complementary RNA are present in nuclei isolated from viroid-infected potato cells

Different oligomeric forms of PSTV are detected in nuclei isolated from PSTV-infected potato cells by means of molecular hybridization, using as probes synthetic oligodeoxyribonucleotides with sequence specificity for (+)PSTV and for (-)PSTV. In addition to several species of longer-than-unit-length (-)PSTV molecules, two oligomeric forms of (+)PSTV are detected, which correspond in size to RNA strands of approximately two and three times viroid unit-length. They must be considered as the precursors of the circular and linear (+)PSTV monomers accumulating in the cell nucleus.

Aphid transmission and a polypeptide are specified by a defined region of the cauliflower mosaic virus genome

Infection of young turnip leaves with an aphid-transmissible isolate, Cabb B-JI, of cauliflower mosaic virus (CaMV) causes synthesis of an Mr 18 000 polypeptide (p18) which co-purifies with virus inclusion bodies. This polypeptide is not detectable in leaves infected with either of two aphid non-transmissible isolates. Campbell and CM4-184. Construction in vitro, of hybrid genomes between Cabb B-JI and Campbell isolates demonstrates that aphid transmissibility and presence of p18 is dependent on the small genome fragment from the BstEII site to the XhoI site. A deletion made in this fragment within open reading frame (ORF) II causes loss of aphid transmissibility and also terminates production of p18. We conclude that aphid transmissibility and the presence of p18 are related to the expression of ORF II of the CaMV genome.

Structural comparisons of some small spherical plant viruses

The structures of tomato bushy stunt virus, southern bean mosaic virus and satellite tobacco necrosis virus have been compared quantitatively. The organization of the shell domains of tomato bushy stunt virus and southern bean mosaic virus within the icosahedral envelope is identical. The wedge-shaped end of the subunit is closer to the fivefold or quasi-sixfold axes in all three viruses but the packing about the three- and twofold axes is quite different in satellite tobacco necrosis virus as compared to tomato bushy stunt virus or southern bean mosaic virus. The polypeptide folds of these viruses have greatest similarity in the beta-sheet region of the eight-stranded anti-parallel beta-barrel. The largest differences occur in the connecting segments. There is no clear indication of homologous amino acid sequences between southern bean mosaic virus and satellite tobacco necrosis virus. However, there is some conservation of the following functional groups. (1) Threonines and serines at the hexagonal-pentagonal wedge-shaped end of the subunit. (2) Lysines and arginines at the protein-RNA interface. (3) Hydrophobic residues in the cavity within the anti-parallel beta-barrel. (4) An aspartic acid near a site which binds Ca in tomato bushy stunt virus. (5) Ionic interactions in the contacts between fivefold-related subunits. These virus coat protein structures are not as similar to each other as the alpha and beta chains of hemoglobin but have greater likeness to one another than the NAD-binding domains of dehydrogenases or lysozymes from hen egg-white and T4 phage. The surface domains of tomato bushy stunt virus and southern bean mosaic virus are more like each other than like satellite tobacco necrosis virus. A divergent evolutionary tree is proposed on the basis of these observations.

Evidence for a restriction/modification-like system in Anacystis nidulans infected by cyanophage AS-1

Anacystis nidulans infected by AS-1 cyanophage contains an endonuclease (AS-1 endonuclease) which splits host DNA but not AS-1 phage DNA [Szekeres, M. (1981) Virology, 111, 1-10]. AS-1 phage DNA proved to be resistant not only to AS-1 endonuclease but also to a number of restriction endonucleases the recognition sites of which contain a central dG-dC dinucleotide. Since an unmodified 5'dG-dC dinucleotide was shown to be present at the sites at which DNA is cleaved by AS-1 endonuclease, the results suggest that the sites attacked preferentially by the AS-1 endonuclease are specifically protected on the AS-1 DNA molecule. The modification of AS-1 DNA was shown to occur specifically in infected Anacystis because AS-1 DNA fragments which are normally resistant to AS-1 endonuclease became susceptible to this enzyme if inserted into pBR322 plasmid and cloned in Escherichia coli. AS-1 DNA was shown to contain about 5% of a modified nucleotide which was not 5-methyldeoxycytidylic acid. Results presented and our earlier data suggest that in Anacystis infected by AS-1 phage, a restriction/modification-like system operates which is able to eliminate 'unwanted' (host) DNA selectively.

Translation of satellite tobacco necrosis virus RNA modified by (not equal to)-r-7,t-8-dihydroxy-t-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene is inhibited in a wheat germ cell-free system

It has been shown that (not equal to)-r-7-,t-8-dihydroxy-t-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE) modification of rabbit globin mRNA results in inhibition of translational initiation. In order to explore the possibility that modification of the 5' cap structure was responsible for this inhibition, the naturally non-capped mRNA from satellite tobacco necrosis virus (STNV) was reacted with BPDE and translated in a wheat germ cell-free system. The extent of modification was 1.3 and 2.9 BPDE residues/molecule. High performance liquid chromatography of the modified nucleosides from enzymatically hydrolyzed STNV RNA revealed that greater than 90% of the nucleoside adducts were substituted at the exocyclic amino group of guanosine. The translational ability of the lower and higher modified STNV, measured by incorporation of [14C]amino acids into acid-precipitable polypeptides is inhibited by 55% and 63%, respectively. Polyacrylamide gel electrophoretic analyses of the translation products indicate that predominantly full-length coat proteins are synthesized but with the carcinogen-modified STNV the amount is reduced. On the other hand, 80S initiation complex formation is not inhibited as measured by binding of the BPDE-modified STNV to ribosomes and followed by glycerol gradient centrifugation. Under these conditions, aurintricarboxylic acid completely inhibits 80S initiation complex formation in the presence of either modified or native STNV. These results suggest that inhibition of in vitro translation of BPDE-modified STNV, in contrast to that of globin mRNA, is not at the level of initiation complex formation but possibly by premature termination of growing polypeptides.

Molecular cloning and characterization of a complete DNA copy of potato spindle tuber viroid RNA

Double-stranded cDNA has been synthesized from RNA of a severe strain of potato spindle tuber viroid using a synthetic oligodeoxyribonucleotide as a primer. Upon cloning in bacteriophage M13mp9, two recombinant phages were selected to construct a pBR322-derived plasmid containing a complete viroid DNA copy. Elucidation of the nucleotide sequence revealed four differences with the previously established sequence of another PSTV strain, three of which were base exchanges and one a deletion.

Viroid RNA is accepted as a template for in vitro transcription by DNA-dependent DNA polymerase I and RNA polymerase from Escherichia coli

The RNA genome of potato spindle tuber viroid (PSTV) is transcribed in vitro into complementary DNA and RNA by DNA-dependent DNA polymerase I and RNA polymerase, respectively, from Escherichia coli. In vitro synthesis of complementary RNA produces distinct transcripts larger than unit length thus reflecting the in vivo mechanism of viroid replication. The influence of varying experimental conditions on the transcription process is studied; actinomycin D is found to drastically reduce complementary RNA synthesis from the PSTV RNA template by RNA polymerase.

Structural transitions in viroid-like RNAs associated with cadang-cadang disease, velvet tobacco mottle virus, and Solanum nodiflorum mottle virus

The conformational transitions of viroid-like RNAs associated with cadang-cadang disease, velvet tobacco mottle virus, and solanum nodiflorum mottle virus were studied by melting analysis and fast temperature jump technique in 1 mM sodium-cacodylate, 10 mM NaCl, 0.1 mM EDTA, pH 6.8. The 4 circular RNAs of cadang-cadang show a highly cooperative transition between 45 and 49 degrees C, respectively, and a second transition of less hypochromicity at about 10 degrees C higher temperatures. The data are interpreted quantitatively on the basis of the sequences and secondary structure models. A very similar scheme for the structure and structural transitions as derived earlier for other viroids applies to the cadang-cadang RNAs. In the main transition the total native secondary structure is disrupted and a stable hairpin consisting of 9 base pairs is newly formed which dissociates in the second transition. The thermal denaturation of the circular RNAs from the viruses mentioned above is clearly distinct from viroid RNA in respect to stability and cooperativity. The results on cadang-cadang RNA are discussed in the light of recent hypotheses about the interference of viroids with the splicing process of the host cell.

Viroids and prions

Viroids are small "naked" infectious RNA molecules that are pathogens of higher plants. The potato spindle tuber viroid (PSTV) is composed of a covalently closed circular RNA molecule containing 359 ribonucleotides. The properties of PSTV were compared with those of the scrapie agent, which causes a degenerative neurological disease in animals. PSTV was inactivated by ribonuclease digestion, psoralen photoadduct formation, Zn2+ -catalyzed hydrolysis, and chemical modification with NH2OH. The scrapie agent resisted inactivation by these procedures, which modify nucleic acids. The scrapie agent was inactivated by proteinase K and trypsin digestion, chemical modification with diethylpyrocarbonate, and by exposure to phenol, NaDodSO4, KSCN, or urea. PSTV resisted inactivation by these procedures, which modify proteins. Earlier evidence suggested that the scrapie agent is smaller than PSTV. Its small size seems to preclude the presence of a genome coding for the protein(s) of a putative capsid. The properties of the scrapie agent distinguish it from both viroids and viruses and have prompted the introduction of the term "prion" to denote a small proteinaceous infectious particle that resists inactivation by procedures that modify nucleic acids.

[Translation of the genomic and subgenomic RNAs of cucumber virus 3 in a cell free system from wheat embryos and in Xenopus laevis oocytes]

The purified preparation of cucumber virus 3 (CV3) (one of the member of tobamovirus group) contains, besides full-length (2.0 X 10(6)) genomic RNA, a short (0.24 X 10(6)) subgenomic RNA coding for coat protein in Xenopus laevis oocytes as well as in the cell-free protein synthesizing system from wheat embryos. The similarity of the polypeptide coded by short CV3 RNA in vitro to natural CV3 coat protein is proved by the similarity of their molecular weights, antigenic specificity and by the similarity of the peptide maps. Individual CV3 genomic RNA coded in vitro for polypeptide 130 X 10(3), and was incapable of coding for the coat protein. The results of translation of an artificial mixture of short and full-length RNAs suggest that it is the short RNA that is preferentially translated.

Evolutionary selection for perfect hairpin structures in viral DNAs

Several recent discoveries have pointed to nucleic acid secondary structure as an additional dimension in gene expression. Further evidence for the formation of hairpins in RNA is the fact that cruciforms exist in negatively supercoiled DNAs. As potential binding sites for proteins, these structures have been proposed to play a part in the regulation of various crucial reactions, such as replication, transcription, or RNA processing. As any random nucleotide sequence can self-anneal with an approximately 50% chance of forming some Watson-Crick-type base pairs, it is difficult to assess which, if any, of all possible hairpin-like secondary structures may be biologically relevant. We have computed the expected distribution of perfectly base-paired structures as a function of loop size and stem length and compared it with the distribution observed in the complete genome of eight DNA viruses from animals, plants and bacteria. We report here that hairpins having six or more consecutive base pairs in the stem are not distributed randomly long the genome, occur much more often than chance would predict, and are particularly over-represented in regions that appear to have regulatory significance. The average loop size was found to decrease with an increase in stem length. These results support our previous hypothesis that these structures are biologically relevant.

Comparative sequence and structure of viroid-like RNAs of two plant viruses

A newly discovered group of spherical plant viruses contains a bipartite genome consisting of a single-strand linear RNA molecule (RNA 1, Mr 1.5 x 10(6) ), and a single-strand, covalently closed circular viroid-like RNA molecule (RNA 2, Mr approximately 125,000). The nucleotide sequences of the RNA 2 of two of these, velvet tobacco mottle virus and solanum nodiflorum mottle virus, have been determined. RNA 2 of solanum nodiflorum mottle virus consists of 377 residues whereas that of velvet tobacco mottle virus consists of two approximately equimolar species, one of 366 residues and the other, with a single nucleotide deletion, of 365 residues. There is 92-95% sequence homology between the RNA 2 species of the two viruses. The predicted secondary structures possess extensive intramolecular base pairing to give rod-like structures similar to those of viroids. The structural similarities between the RNAs 2 of velvet tobacco mottle virus and solanum nodiflorum mottle virus and viroids may reflect functional similarities.

Genetic map of the crown gall suppressive IncW plasmid pSa

A genetic map of the W incompatibility group plasmid pSa has been prepared through the construction of deletion derivatives of pSa and the cloning of various fragments of pSa in pBR322. Phenotypic analysis of these derivatives has identified the location of genes encoding resistance to chloramphenicol, sulfonamides, spectinomycin, streptomycin, kanamycin, gentamycin, and tobramycin. Information sufficient for the replication of the plasmid in both Escherichia coli and Agrobacterium tumefaciens is contained within a 4 kilobase pair region. Two regions have been identified as involved in the transfer of the plasmid; one of these regions is also involved in the inhibition of oncogenesis by pSa when it is present in an oncogenic strain of A. tumefaciens. Certain of the deletion derivatives of pSa are potential vectors for the cloning and analysis of A. tumefaciens Ti plasmid DNA.

Complete nucleotide sequences of the coat protein messenger RNAs of brome mosaic virus and cowpea chlorotic mottle virus

The nucleotide sequences of the subgenomic coat protein messengers (RNA4's) of two related bromoviruses, brome mosaic virus (BMV) and cowpea chlorotic mottle virus (CCMV), have been determined by direct RNA and CDNA sequencing without cloning. BMV RNA4 is 876 b long including a 5' noncoding region of nine nucleotides and a 3' noncoding region of 300 nucleotides. CCMV RNA 4 is 824 b long, including a 5' noncoding region of 10 nucleotides and a 3' noncoding region of 244 nucleotides. The encoded coat proteins are similar in length (188 amino acids for BMV and 189 amino acids for CCMV) and display about 70% homology in their amino acid sequences. Length difference between the two RNAs is due mostly to a single deletion, in CCMV with respect to BMV, of about 57 b immediately following the coding region. Allowing for this deletion the RNAs are indicate that mutations leading to divergence were constrained in the coding region primarily by the requirement of maintaining a favorable coat protein structure and in the 3' noncoding region primarily by the requirement of maintaining a favorable RNA spatial configuration.

Polypeptides induced by tobacco rattle virus during multiplication in tobacco protoplasts

Tobacco protoplasts were irradiated with UV light, inoculated with tobacco rattle virus (TRV), and then cultured in media containing 35S-methionine. Polypeptides induced by TRV infection were detected by PAGE of protein extracts. Three 35S-labeled polypeptides (apparent molecular weights 187,000, 142,000, and 31,000) occurred in extracts of virus-infected protoplasts but not in extracts of buffer-inoculated protoplasts. The 31,000 mol. wt. polypeptides co-migrated with TRV coat protein in polyacrylamide gels and was not detected when inocula contained only the longer particle of TRV. The 187,000 and 142,000 mol. wt. polypeptides migrated in positions very close to products of in vitro translation of TRV RNA-1. Experiments in which 35S-methionine was supplied at different times during multiplication suggested that the bulk of translation of RNA-1 occurred sooner after inoculation than did that of RNA-2.

Nuclear DNA from uninfected or potato spindle tuber viroid-infected tomato plants contains no detectable sequences complementary to cloned double-stranded viroid cDNA

High molecular weight tomato nuclear DNA was isolated from uninfected and potato spindle tuber viroid (PSTV)-infected tomato leaves. Restriction digests were fractionated on agarose gels, denatured and transferred to diazobenzyloxymethylpaper, and hybridized to 32P-labeled cloned double-stranded PSTV cDNA. No hybridization to DNA from either uninfected or infected tissue could be detected under conditions that permitted detection of cloned double-stranded PSTV cDNA at a concentration equivalent to one-fifth copy of PSTV-related DNA per haploid tomato genome. Hybridization of tomato DNA to 32P-labeled cloned soybean 18S and 28S ribosomal DNA sequences showed that the restricted nuclear DNA was suitable for hybridization to probes containing homologous sequences. Our results indicate that neither PSTV nor its complementary strand is transcribed from nuclear DNA but do not rule out the possibility of sequence homology between host DNA and a small portion of PSTV or its complement.

Chrysanthemum stunt viroid: primary sequence and secondary structure

The sequence of the 356 nucleotide residues of chrysanthemum stunt viroid (CSV) has been determined. Overlapping linear viroid fragments were obtained by partial ribonuclease digestion, radiolabelled in vitro at their 5'-ends, and sequenced using partial enzymic cleavage methods. Of the CSV sequence, 69% is contained in the published sequence of potato spindle tuber viroid (PSTV). Differences in the primary sequence of CSV and PSTV suggest that neither the positive nor putative negative strands of these two viroids code for functional polypeptide products. However, the two viroids can form similar secondary structures, implicating a role for viroid structure in replication.

Inhibitor(s) of virus replication (IVR) and localization of viruses in plants

A substance(s) inhibiting virus replication (IVR) is released into the medium from tobacco mosaic virus-infected protoplasts of a cultivar in which the infection in the intact plant is localized. IVR inhibited virus replication in protoplasts from both resistant (Samsun NN) and susceptible (Samsun) plants, when applied up to 18 h after inoculation. It was not produced in protoplasts from susceptible plants or from noninoculated protoplasts of the resistant cultivar. IVR was partially purified using ZnAc2 precipitation, and yielded two biologically active principles with molecular weights of about 26,000 and 56,000 daltons. Preliminary results indicate that IVR inhibits replication of TMV and several other non-related viruses when applied to inoculated leaf disks.

Near identity of 3- RNA secondary structure in bromoviruses and cucumber mosaic virus

The 3- terminal sequences of RNAs 1, 2, 3 and 4 from each of the three bromoviruses (brome mosaic, cowpea chlorotic mottle and broad bean mottle viruses) and also from cucumber mosaic virus display interviral sequence similarity in addition to strong intraviral homology. Interviral similarity is much more evident when RNA secondary, rather than primary, structures are compared. The last 190 bases of the various RNAs can fold into strikingly similar, extensively base-paired secondary structures whose common features are supported by RNA structure mapping. The extreme 3' end of each viral RNA can base-pair in two distinct configurations. Bromovirus RNA 3s each contain an unusually accessible internal oligo(A) sequence which, in brome mosaic virus at least, is located in the intercistronic noncoding region. Functional implications of these structural features are discussed.

Site-specific mutagenesis of Agrobacterium Ti plasmids and transfer of genes to plant cells

A general method is described for the use of tumor-inducing (Ti) plasmids as experimental gene-vectors for plant cells. Intermediate vectors, containing specific Ti plasmid sequences and capable of replication in both E. coli and Agrobacterium strains, were constructed and used for the in vitro introduction of isolated DNA fragments into predetermined sites of the T-region derived fragments. Site-specific inserts and/or deletions-substitutions in Ti plasmids were produced by exchange of the modified T-region sequences for the wild-type sequence by in vivo recombination between intermediate vectors and resident Ti plasmids. This method was applied for the isolation of mutant Ti plasmids affecting either morphogenetic properties or opine synthesis in crown gall tumors. Foreign DNA, inserted at different sites in the T-region of both octopine and nopaline Ti plasmids, was shown to be cotransferred with the T-DNA and to be stably maintained in the transformed plant cells.

Infectivities of native and cloned DNA of cauliflower mosaic virus

Infectivity assays on turnips reveal that (i) cauliflower mosaic virus (CaMV) DNA, whether circular or linear, is as infectious as the complete virus; (ii) linear DNA obtained with restriction enzymes from the native CaMV DNA has the same specific infectivity as when first cloned in plasmid (pBR322) or bacteriophage (lambda gtWES) vectors and then restricted at the cloning site; (iii) in all cases studied mosaic symptoms are accompanied by virus production. DNA isolated from these viruses is again circular and possesses the three "gaps" characteristic of CaMV DNA. The cloned CaMV DNA, when linked to the vector DNA, is noninfectious or exhibits very low infectivity.

Restriction map of native and cloned cauliflower mosaic virus DNA

Cloned CaMV DNA replicates faithfully in Escherichia coli, since the restriction map of the cloned DNA can be superimposed over that of the native viral DNA. However, some short fragments were difficult to detect in the restricted native viral DNA, whereas they formed clear bands when derived from cauliflower mosaic virus (CaMV) DNA clones propagated in the E. coli host. Apparently, the small fragments that carry variable-length single-stranded gaps present only in native viral DNA, give rise to diffuse weak bands difficult to recognize in gels. Comparison of maps for several CaMV strains permits evaluation of their possible evolutionary relationship.

Nucleotide sequence of the putative recognition site for coat protein in the RNAs of alfalfa mosaic virus and tobacco streak virus

The sequence of the 3'-terminal 180 and 140 nucleotides of RNAs 2 and 3, respectively, of tobacco streak virus (TSV) was deduced by reverse transcription in the presence of a specific primer and chain terminators. Homology between the two RNAs was found to be restricted to a 3-terminal region of about 45 nucleotides. The data were compared with the sequence of the homologous region of 145 nucleotides occurring at the 3'-termini of the alfalfa mosaic virus (A1MV) RNAs, which contains the specific binding site for coat protein (Koper-Zwarthoff et al., Nucleic Acids Res. 7, 1887-1900 (1979); Houwing and Jaspars, Biochemistry 17, 2927-2933 (1978)). This was done because of the evidence that the RNAs of A1MV and TSV contain specific binding sites for their own as well as each others coat protein, and that binding of coat protein to these sites is required to initiate infection (Van Vloten-Doting, Virology 65, 215-225 (1975)). The 3'-terminal homologous regions of A1MV and TSV have two features in common: the presence of several stable hairpins and the multiple occurrence of the tetranucleotide sequence AUGC. The hairpins cause the linear array of tandemly repeated AUGC-boxes. It is postulated that the primary interaction of coat protein molecules with the RNAs of AlMV and TSV is a cooperative process involving several binding sites each being composed of a hairpin flanked at its 3'-side by an AUGC-sequence.

Assignment of functions to segments of the DsRNA genome of the Ustilago virus

The genome of the 3 Ustilago maydis viruses, known to be associated with the "killer phenomenon", is segmented. The distribution of the viral functions on different segments has been partly resolved. The reported comparative study, of a series of mutants with deleted segments of the genome and of hybrid variants containing segments of the related viruses, provides additional information on the location of various functions and on the interrelations among the different segments. The data indicates that the functions related to the maintenance of the viral information are located on the H segments. Among these segments some function overlap exists. The maintenance of the M and L segments is dependent on the functions located on the H segments. The functions related to the killer phenotype are distributed on the M2 and L1 segments. These functions include the determination of the killer specificity. The H segments play no role in the determination of the killer specificity and the specificity is determined by the M2 segment. The L segment is essential for the expression of the killer phenotype but it is suggested that the information for the toxin resides in the M2 segment.

Viroids: structure and function

Viroids are nucleic acid species of relatively low molecular weight and unique structure that cause several important diseases of cultivated plants. Similar nucleic acid species may be responsible for certain diseases of animals and humans. Viroids are the smallest known agents of infectious disease. Unlike viral nucleic acids, viroids are not encapsidated. Despite their small size, viroids replicate autonomously in cells of susceptible plant species. Known viroids are single-stranded, covalently closed circular, as well as linear, RNA molecules with extensive regions of intramolecular complementarity; they exist in their native state as highly base-paired rods.

A study of barley stripe mosaic virus (BSMV) genome. I. Determination of sequence homology between BSMV RNA species

The sequence homology between individual RNA species of three-component Norwich strain of BSMV (BSMV-N) has been studied by kinetic hybridization analysis using complementary DNAs obtained for each of the three BSMV-N RNA species by the method of Taylor et al. (1976). No significant sequence homology could be detected between RNA 1, on the one hand, and RNA2 and RNA3, on the other, whereas RNA2 and RNA3 were found to be highly homologous.

Analysis of terminal structures of RNA from potato virus X

The 5'-end structure of potato virus X RNA was determined following enzymatic methylation in vitro. A single 3H-methyl group was introduced into the 2'-position of the 5'-penultimate residue and the end structure was determined as m7GpppG(m)pAp(Xp)3G. This part of the RNA apparently is involved in binding to ribosomes since it can be partially protected against RNase digestion by wheat germ 40S ribosomes. PVX RNA was not retained by poly(U)-sepharose, indicating that it does not contain a 3'-terminal poly(A) tract.

Nucleotide sequence and secondary structure of potato spindle tuber viroid

The viroid of the potato spindle tuber disease (PSTV) is a covalently closed ring of 359 ribonucleotides. As a result of intramolecular base pairing, a serial arrangement of double-helical sections and internal loops form a unique rod-like secondary structure. PSTV is the first pathogen of a eukaryotic organism for which the complete molecular structure has been established.

Homologous nucleotide sequences between prokaryotic and eukaryotic mRNAs: the 5'-end sequence of the mRNA of the lipoprotein of the Escherichia coli outer membrane

The sequence of the first 89 nucleotides at the 5' end of the mRNA for the lipoprotein of the Escherichia coli outer membrane is: GCUACAUGGAGAUUAACUCAAUCU-AGAGGGUAUUAAUAAUGAAAGCUACUAAACUGGUACU-GGGCGCGGUAAUCCUGGGUUCUACUCUG. The sequence of the first 72 nucleotides was established by direct sequencing methods and was extended to 89 residues on the basis of the known sequences of oligonucleotides obtained from complete digestion of the mRNA by ribonuclease T1 or A and the known amino acid sequence of the prolipoprotein. The mRNA has an untranslated region of 38 residues before the initiation codon, AUG. A unique feature of the 5'-end sequence of the mRNA is that the sequence of 12 nucleotides (GUAUUAAUAAUG) prior to, and including, the initiation codon is the same as that found at the ribosome-binding site for 80S ribosomes in brome mosaic virus RNA4, a eukaryotic mRNA [Dasgupta, R., Shih, D., Saris, C. & Kaesberg, P. (1975) Nature 256, 624-628].