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

Analysis of Phyllosphere Microorganisms and Potential Pathogens of Tobacco Leaves

In the tobacco phyllosphere, some of the microbes may have detrimental effects on plant health, while many may be neutral or even beneficial. Some cannot be cultivated, so culture-independent methods are needed to explore microbial diversity. In this study, both metagenetic analysis and traditional culture-dependent methods were used on asymptomatic healthy leaves and symptomatic diseased leaves of tobacco plants. In the culture-independent analysis, asymptomatic leaves had higher microbial diversity and richness than symptomatic leaves. Both asymptomatic and symptomatic leaves contained several potentially pathogenic bacterial and fungal genera. The putative bacterial pathogens, such as species of Pseudomonas, Pantoea, or Ralstonia, and putative fungal pathogens, such as species of Phoma, Cladosporium, Alternaria, Fusarium, Corynespora, and Epicoccum, had a higher relative abundance in symptomatic leaves than asymptomatic leaves. FUNGuild analysis indicated that the foliar fungal community also included endophytes, saprotrophs, epiphytes, parasites, and endosymbionts. PICRUSt analysis showed that the dominant functions of the bacterial community in a symptomatic leaf were cellular processes and environmental information processing. In the other five foliar samples, the dominant functions of the bacterial community were genetic information processing, metabolism, and organismal systems. In the traditional culture-dependent method, 47 fungal strains were isolated from 60 symptomatic tobacco leaf fragments bearing leaf spots. Among them, 21 strains of Colletotrichum (29%), Xylariaceae (14%), Corynespora (14%), Pestalotiopsis (10%), Alternaria (10%), Epicoccum (10%), Byssosphaeria (5%), Phoma (5%), and Diaporthe (5%) all fulfilled Koch’s postulates and were found to cause disease on detached tobacco leaves in artificial inoculation tests. Symptoms on detached leaves caused by three strains of Corynespora cassiicola in artificial inoculation tests were similar to the original disease symptoms in the tobacco field. This study showed that the combined application of culture-dependent and independent methods could give comprehensive insights into microbial composition that each method alone did not reveal.

Virus Host Jumping Can Be Boosted by Adaptation to a Bridge Plant Species

Understanding biological mechanisms that regulate emergence of viral diseases, in particular those events engaging cross-species pathogens spillover, is becoming increasingly important in virology. Species barrier jumping has been extensively studied in animal viruses, and the critical role of a suitable intermediate host in animal viruses-generated human pandemics is highly topical. However, studies on host jumping involving plant viruses have been focused on shifting intra-species, leaving aside the putative role of “bridge hosts” in facilitating interspecies crossing. Here, we take advantage of several VPg mutants, derived from a chimeric construct of the potyvirus Plum pox virus (PPV), analyzing its differential behaviour in three herbaceous species. Our results showed that two VPg mutations in a Nicotiana clevelandii-adapted virus, emerged during adaptation to the bridge-host Arabidopsis thaliana, drastically prompted partial adaptation to Chenopodium foetidum. Although both changes are expected to facilitate productive interactions with eIF(iso)4E, polymorphims detected in PPV VPg and the three eIF(iso)4E studied, extrapolated to a recent VPg:eIF4E structural model, suggested that two adaptation ways can be operating. Remarkably, we found that VPg mutations driving host-range expansion in two non-related species, not only are not associated with cost trade-off constraints in the original host, but also improve fitness on it.

CRISPR/Cas13a targeting of RNA virus in plants

KEY MESSAGE

This approach is quite promising to control plant viral diseases and create synthetic networks to better understand the structure/function relationship in RNA and proteins. Plant viruses are obligate intracellular parasites which causes enormous losses in crop yield worldwide. These viruses replicate into infected cells by highjacking host cellular machinery. Over the last two decades, diverse approaches such as conventional breeding, transgenic approach and gene silencing strategies have been used to control RNA viruses, but escaped due to high rate of mutation. Recently, a novel CRISPR enzyme, called Cas13a, has been used engineered to confer RNA viruses resistance in plants. Here, we summarize the recent breakthrough of CRISPR/Cas13a and its applications in RNA biology.

Molecular biology of potyviruses

Potyvirus is the largest genus of plant viruses causing significant losses in a wide range of crops. Potyviruses are aphid transmitted in a nonpersistent manner and some of them are also seed transmitted. As important pathogens, potyviruses are much more studied than other plant viruses belonging to other genera and their study covers many aspects of plant virology, such as functional characterization of viral proteins, molecular interaction with hosts and vectors, structure, taxonomy, evolution, epidemiology, and diagnosis. Biotechnological applications of potyviruses are also being explored. During this last decade, substantial advances have been made in the understanding of the molecular biology of these viruses and the functions of their various proteins. After a general presentation on the family Potyviridae and the potyviral proteins, we present an update of the knowledge on potyvirus multiplication, movement, and transmission and on potyvirus/plant compatible interactions including pathogenicity and symptom determinants. We end the review providing information on biotechnological applications of potyviruses.

Development of a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of Sugarcane mosaic virus and Sorghum mosaic virus in sugarcane

A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detecting Sugarcane mosaic virus (SCMV) and Sorghum mosaic virus (SrMV) in sugarcane. Six sets of four primers corresponding to the conserved coat protein gene were designed and tested for each virus. Three primer sets designed for detecting SCMV and four for detecting SrMV were successful in the RT-LAMP assay. The effective primer sets were not only specific for their target virus, but also able to detect multiple virus strains. The magnesium sulfate concentration of the reaction solution was optimized, with both viruses requiring a minimum of 5mM for detection. The sensitivity of this RT-LAMP assay was less than that of conventional and real-time RT-PCR.

Helical viruses

Virtually all studies of structure and assembly of viral filaments have been made on plant and bacterial viruses. Structures have been determined using fiber diffraction methods at high enough resolution to construct reliable molecular models or several of the rigid plant tobamoviruses (related to tobacco mosaic virus, TMV) and the filamentous bacteriophages including Pf1 and fd. Lower-resolution structures have been determined for a number of flexible filamentous plant viruses using fiber diffraction and cryo-electron microscopy. Virions of filamentous viruses have numerous mechanical functions, including cell entry, viral disassembly, viral assembly, and cell exit. The plant viruses, which infect multicellular organisms, also use virions or virion-like assemblies for transport within the host. Plant viruses are generally self-assembling; filamentous bacteriophage assembly is combined with secretion from the host cell, using a complex molecular machine. Tobamoviruses and other plant viruses disassemble concomitantly with translation, by various mechanisms and involving various viral and host assemblies. Plant virus movement within the host also makes use of a variety of viral proteins and modified host assemblies.

The nucleotide sequence of the coding region of tobacco etch virus genomic RNA: evidence for the synthesis of a single polyprotein

The complete nucleotide sequence of the tobacco etch virus (TEV) RNA genome has been determined excepting only the nucleotide(s) present at the extreme 5' terminus. The assembled TEV genomic sequence is 9496 nucleotides in length followed by a polyadenylated tract ranging from 20 to 140 residues. A computer search of the sequence reveals the following. A 5' untranslated region, rich in adenosine and uridine, is present between nucleotides 1 and 144. A putative initiation codon, at nucleotides 145-147, marks the beginning of a large open-reading frame (ORF) which ends with an opal (UGA) termination codon at positions 9307-9309. A 186-nucleotide untranslated region is present between the termination codon of the ORF and the beginning of the 3' polyadenylated region. The predicted translation product of this ORF is a 3054 amino acid polyprotein with a mol wt of 345,943. A function for the large (54,000 Mr) nuclear inclusion protein is suggested by a comparison of the deduced amino acid sequence with a protein data bank. This protein displays biochemical similarities to other viral RNA-dependent, RNA polymerases.

Processing of the tobacco etch virus 49K protease requires autoproteolysis

The final products encoded by the tobacco etch virus genome arise by proteolytic cleavage of a single large polyprotein precursor. Processing of the polyprotein at several sites requires the activity of a viral protease of 49,000 molecular weight (49K). We have examined the excision of the 49K protease from polyproteins translated from defined RNA transcripts. Polyproteins containing an intact 49K protein were efficiently processed after synthesis in a rabbit reticulocyte lysate to yield the 49K product. Introduction of a single amino acid substitution (cysteine to alanine) at the putative active site of the 49K protease abolished processing, indicating that the protease was excised from the polyprotein via an autocatalytic mechanism. Release of the 49K protease was determined to require autoproteolysis, since synthetic polyproteins which contained either or both 49K cleavage sites were processed poorly, if at all, in trans reactions. Protein microsequence analysis revealed that processing in vitro occurred between a glutamine-glycine dipeptide to generate the 49K amino terminus.

Translation of papaya ringspot virus RNA in vitro: detection of a possible polyprotein that is processed for capsid protein, cylindrical-inclusion protein, and amorphous-inclusion protein

The genomic RNA of papaya ringspot virus (PRV), a member of the potyvirus group, was translated in a rabbit reticulocyte cell-free system as an approach to determining the translation strategy of the virus. The RNA directed synthesis of more than 20 distinct polypeptides ranging from apparent molecular weight of 26,000 (26K) to 220K. Antiserum to PRV capsid protein (CP) reacted with a subset of these polypeptides, including a 36K protein that comigrated with PRV CP during electrophoresis. Immunoprecipitation with antiserum to PRV cylindrical-inclusion protein (CIP) defined another set of polypeptides including 70K, 108K, 205K, and 220K proteins as major precipitates. The 70K protein comigrated with authentic CIP, and the 205K and 220K proteins were related to both CP and CIP. Immunoprecipitation with antiserum to PRV amorphous-inclusion protein (AIP) defined a unique set of polypeptides which contained a 112K protein as the major precipitate and 51K, 65K, and 86K proteins as minor precipitates. The 51K protein comigrated with authentic AIR A major product of 330K was observed when translation was done without the reducing agent, dithiothreitol. Immunological analyses and kinetic studies indicated that the 330K protein zone was related to the presumed CP, CIP, and AIP zones and 330K possibly is the common precursor for these viral proteins. The presence of a polyprotein of Mr corresponding to the entire coding capacity of the genomic RNA and its likely precursor relationship to the other polypeptides suggest that proteolytic processing is involved in the translation of PRV RNA.

Three heterologous proteins simultaneously expressed from a chimeric potyvirus: infectivity, stability and the correlation of genome and virion lengths

Three heterologous proteins were simultaneously expressed from a chimeric potyvirus Potato virus A (PVA) in Nicotiana benthamiana. The genes for green fluorescent protein of Aequoria victoriae ("G"; 714 nucleotides, nt), luciferase of Renilla reniformis ("L", 933 nt) and beta-glucuronidase of Escherichia coli ("U", 1806 nt) were inserted into the engineered cloning sites at the N-terminus of the P1 domain, the junction of P1 and helper component protein (HC-Pro), and the junction of the viral replicase (NIb) and coat protein (CP), respectively, in an infectious PVA cDNA. The proteins were expressed as part of the viral polyprotein and subsequently released by cleavage at the flanking proteolytic cleavage sites by P1 (one site) or the NIa-Pro proteinase (other sites). The engineered viral genome (pGLU, 13311 nt) was 39.2% larger than wild-type PVA (9565 nt) and infected plants of N. benthamiana systemically. pGLU was stable and expressed all three heterologous proteins, also following the second infection cycle initiated by sap-inoculation of new plants with the progeny viruses. The gene for GUS showed some inherent instabilities, as also reported in other studies. Accumulation of pGLU in infected leaves was lower by a magnitude as compared to the vector viruses pG0U and p0LU used to express two heterologous proteins. Hence, pGLU may have reached the maximum genome size that can still function and complete the PVA infection cycle. Examination of virions by electron microscopy indicated that the virion lengths of PVA chimera with various numbers of inserts were directly proportional to their genome lengths.

Detection of the potyviral genome-linked protein VPg in virions and its phosphorylation by host kinases

The multifunctional genome-linked protein (VPg) of Potato virus A (PVA; genus Potyvirus) was found to be phosphorylated as a part of the virus particle by a cellular kinase activity from tobacco. Immunoprecipitation, immunolabeling, and immunoelectron microscopy experiments showed that VPg is exposed at one end of the virion and it is accessible to protein-protein interactions. Substitution Ser185Leu at the C-proximal part of VPg reduces accumulation of PVA in inoculated leaves of the wild potato species Solanum commersonii and delays systemic infection, which is not observed in tobacco plants. Our data show that kinases of S. commersonii differentially recognize the VPg containing Ser or Leu at position 185, whereas both forms of VPg are similarly recognized by tobacco kinases. Taken together, our data imply that the virion-bound VPg may interact with host proteins and that phosphorylation of VPg may play a role in the VPg-mediated functions during the infection cycle of potyviruses.

Mapping of viral genomic regions important in cross-protection between strains of a potyvirus

Cross-protection was tested between potato and tobacco strains of Potato virus A, a member of the genus Potyvirus (PVA), in tobacco plants. Cross-protection was effective only at the initiation of infection. The potato strains provided only weak cross-protection against the tobacco strain, whereas the tobacco strain provided strong cross-protection against potato strains. The tamarillo strain (TamMV) showed cross-protection phenotypes mostly resembling those of the potato strains. Chimera of the PVA strains were utilized to map viral genomic regions important for cross-protection. The coat protein (CP) encoding region and the helper component proteinase (HCpro) affected cross-protection and virus accumulation. An amino acid substitution at the CP N-terminus reduced virus accumulation and the ability to overcome cross-protection, whereas amino acid substitutions introduced to the HCpro increased virus accumulation and the ability to overcome cross-protection. Closer sequence relatedness between the protector and challenger isolate, as determined by the CP-encoding sequence, was correlated with an increased cross-protection ability. Cross-protection was not overcome by inoculation with nonencapsidated viral RNA. Thus, the differences in cross-protection abilities between PVA strains and chimera were not explained with the "re-encapsidation model" described for strains of Tobacco mosaic tobamovirus but may be associated with a virus infection-induced RNA silencing mechanism.

Identification of the genome-linked protein in virions of Potato virus A, with comparison to other members in genus Potyvirus

Viruses of the genus Potyvirus, the largest genus of plant-infecting viruses, have a messenger-polarity ssRNA genome encapsidated by approximately 2000 units of the viral coat protein (CP), resulting in filamentous virions. Only few studies have examined potyvirus virions for the presence of other structural proteins. A protein linked covalently to the 5'-end of the genome has been identified in Tobacco vein mottling virus (TVMV) and Tobacco etch virus (TEV). In TEV, it is either the viral NIa protein or only its N-terminal domain (VPg) separated autocatalytically from the C-terminal proteinase domain (NIa-Pro). Virions of TVMV carry only the VPg. We examined virions of Potato virus A (PVA) for the genome-linked protein using immunoblotting or iodination and immunoprecipitation. The VPg ( approximately 25 kDa) only, and not the unprocessed NIa, was detected. Another signal corresponding to approximately 49 kDa was detected in disrupted, RNase-treated virions with anti-VPg antibodies but not with antibodies to NIa-Pro. Since it possibly represented a dimeric form of the VPg, self-interaction of the VPg was tested using the yeast two-hybrid system, which showed that the VPg self-interacts in the absence of viral RNA.

Potyvirus genome-linked protein (VPg) determines pea seed-borne mosaic virus pathotype-specific virulence in Pisum sativum

The mechanism of Pisum sativum pathotype-specific resistance to pea seed-borne mosaic potyvirus (PSbMV) was investigated and the coding region determinant of PSbMV virulence was defined. Homozygous recessive sbm-1 peas are unable to support replication of PSbMV pathotype 1 (P-1), whereas biochemically and serologically related pathotype 4 (P-4) is fully infectious in the sbm-1/sbm-1 genotype. We were unable to detect viral coat protein or RNA with double antibody sandwich-enzyme-linked immunosorbent assay and reverse transcription-polymerase chain reaction in sbm-1/sbm-1 P-1-inoculated protoplasts and plants. Lack of viral coat protein or RNA in P-1 transfected sbm-1/sbm-1 protoplasts suggests that sbm-1 resistance is occurring at the cellular level and that inhibition of cell-to-cell virus movement is not the operating form of resistance. In addition, because virus products were not detected at any time post-inoculation, resistance must either be constitutive or expressed very early in the virus infection process. P-1-resistant peas challenged with full-length, infectious P-1/P-4 recombinant clones demonstrated that a specific P-4 coding region, the 21-kDa, genome-linked protein (VPg), was capable of overcoming sbm-1 resistance, whereas clones containing the P-1 VPg coding region were noninfectious to sbm-1/sbm-1 peas. VPg is believed to be involved in potyvirus replication and its identification as the PSbMV determinant of infectivity in sbm-1/sbm-1 peas is consistent with disruption of an early P-1 replication event.

High level production of potyvirus-like particles in insect cells infected with recombinant baculovirus

The full length gene for the coat protein (CP) of the potyvirus, Johnsongrass mosaic virus, was incorporated into recombinant baculovirus and expressed in insect cells. Western blot and Coomassie-stained polyacrylamide gel electrophoresis analysis of infected insect cells demonstrated that CP was produced in large quantity. Electron microscopic examination of these cells showed the presence of numerous potyvirus-like particles in the cytoplasm. Morphologically the particles resembled potyvirus particles assembled in vitro in the absence of viral RNA and those found in Escherichia coli expressing the recombinant CP gene.

The 5' untranslated region of PVY RNA, even located in an internal position, enables initiation of translation

Potato virus Y (PVY) is the type member of the potyvirus group. Potyviruses, like picorna-, como-, and nepoviruses, belong to the picornavirus-like supergroup. All these viral RNAs have a VPg at their 5' end, and for four picornaviruses and one comovirus internal initiation of translation has been reported. To know if such a translational mechanism holds true for potyviral RNAs, the 5' nontranslated region (NTR) of PVY RNA was placed in an internal position, either by adding 91 bases upstream of the PVY 5'NTR or by inserting the PVY 5'NTR into an intercistronic region. The addition of extra bases stimulates translation in a rabbit reticulocyte lysate, and the presence of the PVY 5'NTR in the intercistronic region allows the synthesis of the second cistron. These findings strongly suggest that PVY RNA initiates translation by an internal ribosome-binding mechanism. Furthermore, the use of antisense oligodeoxynucleotides indicates that the entire 5'NTR seems to be involved in such a mechanism.

Expression of the "helper component" protein of potato virus Y (PVY) in E. coli: possible involvement of a third protease

Transmission of potyviruses by aphids depends on the presence of a virus encoded helper-component protein (HC) that also exhibits protease activity. HC was expressed in E. coli from two types of clones: a full-length cDNA clone of PVY and two 5' end clones containing the first three cistrons (3.6-3.7 kbp). The clones derived from the 5' end of PVY expressed HC of the size of the mature component. Other proteins reacting with antibodies to HC were also observed, and their sizes corresponded with those of expected intermediates resulting from partial protease cleavage of the three-cistron polyprotein. On the other hand, the only detectable HC-related product of the full-length clone was a mature-size HC. The presence of a third PVY protease among the first three cistrons is therefore suggested.

Expression and assembly of the potato virus Y (PVY) coat protein (CP) in Escherichia coli cells

A clone harboring the full-length cDNA of potato virus Y in a lambda-DASH vector under the control of a T7 promoter was introduced into Escherichia coli carrying the T7-RNA-polymerase gene on a plasmid. The viral coat protein was expressed and the product was of the same size as the corresponding mature protein in infected plants. Immunoelectronmicroscopy of transfected cell extracts revealed virus-like particles, indicating that the proteins involved in its processing and the viral coat protein retained their native activity.

Cloning, sequencing, and expression in Escherichia coli of the coat protein gene of a new potyvirus infection South African Passiflora

Complementary DNA representing 1418 nucleotides (nt) of the 3'-poly(A)-proximal tract of the genomic RNA of a potyvirus causing woodiness disease in South African passion fruit, was cloned and sequenced. The sequence contained a single long open reading frame (ORF) of 1188 nt with no initiation codon, and a 3'-non-coding region (3'-NCR) of 230 nt followed by a poly-adenylate tract. Comparison of the ORF with other potyviral coat protein (CP) sequences led to the prediction that a 279 residue CP of MW 31722 is encoded by 836 nt at the 3'-terminus of the ORF. This virus is not merely a South African strain of passion fruit woodiness virus (PWV): the deduced CP sequence is only distantly related to CPs of other sequenced strains of PWV, although it is part of a distinct subgroup of potyviruses related to PWV. The virus was therefore designated as South African passiflora virus (SAPV). The DNA containing the putative CP was cloned into the pUEX2 bacterial expression vector and expressed in Escherichia coli as a beta-gal-CP fusion protein. The fusion protein reacted with polyclonal antisera raised against the native virus, and antisera raised against partially purified fusion protein reacted with viral CP in Western blots.

A polymerase chain reaction method adapted for selective amplification and cloning of 3' sequences of potyviral genomes: application to dasheen mosaic virus

'Universal' degenerate oligonucleotide primers were used to amplify cDNA sequences containing the 3' untranslated region (3' UTR) and a portion of the coat protein gene sequence of dasheen mosaic potyvirus (DMV). These primers were based on the conserved WCIEN and QMKAAA 'boxes' of the potyviral coat protein and the poly-A tail found at the 3' end of the genome. The forward genome-sense primers were designed taking into consideration the codon degeneracy of the WCIEN and QMKAAA residues for several potyviruses. The anti-sense reverse primer has 21 T residues followed by either A, C or G at the 3' end to ensure specific priming at the end of the 3' UTR and beginning of the poly-A tail. The specificity of amplification was verified using the known potyviruses (watermelon mosaic 2 and soybean mosaic viruses). To demonstrate the applicability of this method, the 3' UTR of the unsequenced DMV was amplified, cloned and sequenced. Sequence comparisons with other potyviral 3' UTRs revealed DMV to be quite distinct: nucleotide sequence similarities of only 34% to 44% were found with sequenced viruses indicating no close affinities with any other potyvirus. The potyvirus 3' sequence amplification procedure is simple and rapid, is potentially useful in developing virus specific probes and may be used to differentiate strains and species of potyviruses on the basis of the 3' UTR sequences.

Characterization of the potyviral HC-pro autoproteolytic cleavage site

The helper component-proteinase (HC-Pro) encoded by potyviruses functions to cleave the viral polyprotein by an autoproteolytic mechanism at the HC-Pro C-terminus. This protein belongs to a group of viral cysteine-type proteinases and has been shown previously to catalyze proteolysis between a Gly-Gly dipeptide. The amino acid sequence requirements surrounding the HC-Pro C-terminal cleavage site of the tobacco etch virus polyprotein have been investigated using site-directed mutagenesis and in vitro expression systems. A total of 51 polyprotein derivatives, each differing by the substitution of a single amino acid between the P5 and P2' positions, were tested for autoproteolytic activity. Substitutions of Tyr (P4), Val (P2), Gly (P1), and Gly (P1') were found to eliminate or nearly eliminate proteolysis. Substitutions of Thr (P5), Asn (P3), and Met (P2'), on the other hand, were permissive for proteolysis, although the apparent processing rates of some polyproteins containing these alterations were reduced. These results suggest that auto-recognition by HC-Pro involves the interaction of the enzymatic binding site with four amino acids surrounding the cleavage site. Comparison of the homologous sequences of five potyviral polyproteins revealed that the residues essential for processing are strictly conserved, whereas the nonessential residues are divergent. The relationship between HC-Pro and other viral and cellular cysteine-type proteinases is discussed.

The general properties of potyviruses

The criteria used during the past three decades for including viruses in the potyvirus group are briefly discussed and evaluated. The biological and physico-chemical properties of the viruses transmitted by aphids, mites, whiteflies, or the fungus Polymyxa graminis are reviewed, and the taxonomic value of their molecular properties in regrouping the viruses into four groups or genera within the family Potyviridae is discussed.

Effects of antisense oligodeoxynucleotide hybridization on in vitro translation of potato virus Y RNA

Potato virus Y (PVY), a potyvirus, has an RNA genome containing 9704 nucleotides of which 185 belong to the 5' nontranslated region (NTR). Contrary to most eukaryotic mRNAs that have a cap structure, the potyvirus RNA has a genome-linked protein (VPg). In order to understand the mechanisms of PVY RNA translation initiation, hybrid-arrest translation was used to localize sequences involved in binding of proteins and/or ribosomes. The 5' NTR was fused to the beta-glucuronidase (GUS) reporter gene. Six antisense oligodeoxynucleotides were used for hybridization, and the efficiency of the in vitro translation of the hybridized mRNA was modified to different levels depending upon the position of the oligodeoxynucleotide used. The highest inhibition was obtained with an oligodeoxynucleotide hybridized to the 5' end. In addition, translation of GUS mRNA containing the PVY 5' NTR was greatly enhanced when this mRNA was capped. These results differ from those obtained with the tobacco etch virus (TEV) and three picornaviruses, but are similar to those obtained with capped mRNA.

Two newly detected nonstructural viral proteins in potyvirus-infected cells

The existence of two viral RNA-encoded proteins in cells infected with tobacco vein mottling potyvirus (TVMV) has been demonstrated. One of the proteins (named 34K) maps at the N-terminus of the TVMV polyprotein and the other (42K) between the helper component and cylindrical inclusion proteins; both had previously been predicted in the consensus potyviral genetic map. The 34K and 42K coding regions of TVMV were cloned separately in a bacterial expression vector and the proteins were isolated from transformed Escherichia coli. These were used to raise polyclonal antibodies which reacted specifically with proteins of the expected size in immunoblots of extracts of TVMV-infected tobacco leaves and protoplasts. In addition to 42K, the anti-42K serum detected similar amounts of a second protein of apparent size 37 kDa that was absent in 42K-expressing bacteria. Both 34K and 42K were present predominantly in membrane-enriched fractions of extracts of TVMV-infected tobacco leaves. Computer analysis of the deduced amino acid sequence of 42K suggests that this viral protein may be an integral transmembrane protein.

Nucleotide sequence of the 3' terminal region of lettuce mosaic potyvirus RNA shows a Gln/Val dipeptide at the cleavage site between the polymerase and the coat protein

DNA complementary to the 3' terminal 1651 nucleotides of the genome of the common strain of lettuce mosaic virus (LMV-O) has been cloned and sequenced. Microsequencing of the N-terminus enabled localization of the coat protein gene in this sequence. It showed also that the LMV coat protein coding region is at the 3' end of the genome, and that the coat protein is processed from a larger protein by cleavage at an unusual Q/V dipeptide between the polymerase and the coat protein. This is the first report of such a site for cleavage of a potyvirus polyprotein, where only Q/A, Q/S, and Q/G cleavage sites have been reported. The LMV coat protein gene encodes a 278 amino acid polypeptide with a calculated Mr of 31,171 and is flanked by a region which has a high degree of homology with the putative polymerase and a 3' untranslated region of 211 nucleotides in length. Percentage of homology with the coat protein of other potyviruses confirms that LMV is a distinct member of this group. Moreover, amino acid homologies noticed with the coat protein of potexvirus, bymovirus, and carlavirus elongated plant viruses suggest a functional significance for the conserved domains.

The VPg of tobacco etch virus RNA is the 49-kDa proteinase or the N-terminal 24-kDa part of the proteinase

Preparations of tobacco etch virus (TEV) RNA which were purified by sucrose gradient centrifugation, digested with RNase, and analyzed by SDS-polyacrylamide gel electrophoresis contained proteins of 49, 32, and 24 kDa. The 49- and 24-kDa proteins reacted with polyclonal antiserum to the TEV 49-kDa proteinase while the 32-kDa protein reacted with anti-TEV serum. Further purification of the RNA by centrifugation through CsCl removed the coat protein (32 kDa), but not the 49- and 24-kDa proteins. The 49- and 24-kDa proteins did not migrate into a polyacrylamdie gel when the RNA was not digested with RNase. These results indicate that the VPg of TEV is either the 49-kDa proteinase or the 24 kDa that represents the amino-terminal half thereof.

Determination of polyprotein processing sites by amino terminal sequencing of nonstructural proteins encoded by plum pox potyvirus

Nonstructural proteins of plum pox potyvirus were partially purified following a procedure described for the isolation of tobacco etch virus nuclear inclusion proteins. Plum pox virus proteins with electrophoretic mobilities corresponding to 49, 59 and 68 kDa reacted with antibodies against the 49 kDa and 54 kDa components of the nuclear inclusions and the 70 kDa component of the cylindrical inclusions of tobacco etch virus, respectively. Further purification by size exclusion high performance liquid chromatography or SDS-polyacrylamide gel electrophoresis, and amino terminal amino acid sequencing permitted the location in the plum pox virus polyprotein of the cleavage sites from which the 49 kDa (NIa-type, protease), 59 kDa (NIb-type, putative RNA replicase), and 68 kDa (CI-type) proteins originate. A 110 kDa protein which copurified with the plum pox virus inclusion proteins reacted with both anti-NIa and anti-NIb sera and had the same amino terminus as the plum pox virus 49 kDa protein, indicating that it is a non-processed 49-59 kDa polypeptide.

Identification of essential residues in potyvirus proteinase HC-Pro by site-directed mutagenesis

Two virus-encoded proteinases are responsible for proteolysis of potyvirus polyproteins. One of these, HC-Pro, is a multifunctional protein that autolytically cleaves at its carboxyl-terminus (J.C. Carrington et al., 1989, EMBO J. 8, 365-370). To identify the class of proteinase to which HC-Pro belongs, tobacco etch virus (TEV) HC-Pro mutants containing single amino acid substitutions at serine, cysteine, aspartic acid, and histidine positions were synthesized by in vitro transcription and translation and were tested for autoproteolytic activity. Combinations of these residues are constituents of the active sites of diverse groups of cellular and viral proteinases. Only those positions that were strictly conserved among four potyvirus HC-Pro proteolytic domains (for which sequences have been deduced) were mutagenized. Of the 19 mutant proteinases synthesized and tested, only those with alterations at Cys-649 and His-722 were defective for HC-Pro autolytic activity. Most of the other mutant proteinases exhibited no impairments in processing kinetics experiments. The spectrum of essential residues, as defined by this genetic analysis, supports the hypothesis that HC-Pro most closely resembles members of the cysteine-type family of proteinases.

Bean mild mosaic virus: genome and its translation products

Viral RNA from purified preparations of bean mild mosaic virus (BMMV) was resolved into two RNAs of mol. wt 1.5 X 10(6) daltons (R1) and 0.76 X 10(6) daltons (R2). Complementary DNA hybridizations, infectivity tests, and in-vitro translation studies established that R2 is a subgenomic RNA derived from R1. In-vitro translation studies showed that the genomic RNA (R1) coded for two major proteins of mol. wt. 40.5 kD and 25.7 kD. Of these, the 40.5 kD protein was shown to be the capsid protein that is translated in vitro from both the R1 and R2 RNAs. Time-course studies on the appearance of in-vitro translation products showed that the 25.7 kD product is the earliest product made when the genomic R1 RNA is translated. This is not one of the products of R2 RNA. Several of the characteristics of BMMV described in this paper show similarities with turnip crinkle virus (TCV) and carnation mottle virus (CarMV).

Mutational analysis of tobacco etch virus polyprotein processing: cis and trans proteolytic activities of polyproteins containing the 49-kilodalton proteinase

The genome of tobacco etch virus contains a single open reading frame with the potential to encode a 346-kilodalton (kDa) polyprotein. The large polyprotein is cleaved at several positions by a tobacco etch virus genome-encoded, 49-kDa proteinase. The locations of the 49-kDa proteinase-mediated cleavage sites flanking the 71-kDa cytoplasmic pinwheel inclusion protein, 6-kDa protein, 49-kDa proteinase, and 58-kDa putative polymerase have been determined by using cell-free expression, proteolytic processing, and site-directed mutagenesis systems. Each of these sites is characterized by the conserved sequence motif Glu-Xaa-Xaa-Tyr-Xaa-Gln-Ser or Gly (in which cleavage occurs after the Gln residue). The amino acid residue (Gln) predicted to occupy the -1 position relative to the scissile bond has been substituted, by mutagenesis of cloned cDNA, at each of four cleavage sites. The altered sites were not cleaved by the 49-kDa proteinase. A series of synthetic polyproteins that contained the 49-kDa proteinase linked to adjoining proteins via defective cleavage sites were expressed, and their proteolytic activities were analyzed. As part of a polyprotein, the proteinase was found to exhibit cis (intramolecular) and trans (intermolecular) activity.

Mapping of the tobacco vein mottling virus VPg cistron

The location of the cistron encoding the genome-linked protein (VPg) in the potyvirus tobacco vein mottling virus (TVMV) was investigated. Precipitation of 125I-labeled VPg with anti-tobacco etch virus 49K nuclear inclusion protein antiserum (which reacts with the NIa nuclear inclusion protein of TVMV) indicated that the TVMV VPg is immunologically related to NIa. Lysyl residues were found to be present at positions 2, 11, and 16 of the amino-terminal region of the VPg. A search of the TVMV polyprotein sequence for this distribution of lysyl residues revealed a unique location beginning at amino acid residue 1801, the proposed amino-terminus of the NIa protein.

Characterization of repetitive elements in several Cucurbita species

About 1.3×10(5) copies of a tandemly arranged, 351 base pair element constitute from 4 to 8% of the Cucurbita pepo genome. A homologous, high copy number repetitive element is present in the genomes of C. moschata and C. foetidissima, but not in C. maxima or Cucumis sativus. Array lengths of at least 65 members have been detected for C. pepo, and 140 for C. moschata. The nucleotide sequence of six C. pepo repeat units were determined and each was found to be unique, differing from the others at from 7 to 23 positions. The element was composed of highly modified DNA as evidenced by the fact that only one of its two Hpa I restriction sites is subject to digestion and by the observation that all internal Cs and about half of the external Cs of its single Hpa II site are methylated. At least 5 cellular RNA species contain sequences complementary to one of the DNA strands of the element. These have discrete sizes of 3.0, 2.3, 1.8, 1.3 and 0.5 kb. Such transcripts are detected in C. pepo, C. moschata and C. foetidissima stem and/or leaf RNA, but not root RNA and are probably not polyadenylated. No transcripts were found which contain sequences complementary to the other DNA strand of the element.

On the inhibition of plant virus multiplication by ribavirin

The inhibition of the replication of potato virus X (PVX), belladonna mottle virus, tobacco mosaic virus, potato virus Y (PVY), and tobacco necrosis virus by ribavirin and pyrazofurin is described with emphasis on the inhibition of PVX by ribavirin. Ribavirin inhibits an early step of PVX replication. The inhibition is reversed to different degrees by all ribo- and deoxyribonucleosides, most strongly by thymidine. In tobacco leaves, nucleosides compete with ribavirin for phosphorylation to monophosphate by a nucleoside phosphotransferase. However, the final and main phosphorylation product of ribavirin is triphosphate. It is suggested that ribavirin triphosphate is the antiviral form and that it acts by inhibiting the capping of viral RNAs. This mode of action cannot be applied to the inhibition of PVY, the RNA of which is probably covalently linked to a protein at the 5'-terminus.

Association of tobacco etch virus related RNA with chloroplasts in extracts of infected plants

The RNA in various subcellular fractions of tobacco etch virus (TEV) infected tissue was analyzed for the presence of complementary viral RNA, and double-stranded viral RNA by hybridization with 32P-labeled viral RNA or cDNA probes. Although viral RNA was detected in several cellular fractions, the complementary RNA of full-length size was found exclusively associated with fractions containing chloroplasts. Treatment of RNAs with RNase before hybridization suggested that the virus-related complementary RNA was present in double-stranded form.

Complementary DNA cloning and expression of the papaya ringspot potyvirus sequences encoding capsid protein and a nuclear inclusion-like protein in Escherichia coli

Three cDNA clones that express viral gene products in Escherichia coli JM83 were derived from a watermelon mosaic virus-1 strain of papaya ringspot virus (PRSV-W). DNAs complementary to portions of the viral RNA were inserted into the pUC8 and pUC9 plasmids, and the expressed polypeptides were fusion products with the amino terminus of beta-galactosidase. Clones W1-77 and W2-1 expressed fusion products with apparent molecular weights of 40,000 (40K) and 14K, respectively, which were serologically related to PRSV capsid protein. A 52K product serologically related to a 54K nuclear inclusion protein of tobacco etch virus was produced by clone W1-18. The sequences encoding the capsid and 57K nuclear inclusion-like proteins of PRSV were physically mapped to adjacent positions through Southern blot analyses of clones W1-77 and W1-18.

The H protein isolated from tobacco mosaic virus reassociates with virions reconstituted in vitro

Virions of two strains of tobacco mosaic virus (U1 and Cc) have associated with them a small amount of a minor protein called H protein (A. Asselin and M. Zaitlin, 1978, Virology 91, 173-181), now known to be related to the viral coat protein (C.W. Collmer, V.M. Vogt, and M. Zaitlin, 1983, Virology 126, 429-448.). In the present study, a quantification technique involving disruption of virions followed by direct analysis of the component parts on SDS polyacrylamide gels was used to confirm an average of one molecule of H protein per virion for U1 TMV. H protein was separated from coat protein and purified by electrofocusing in a flatbed of granulated gel under stringent dissociating conditions. When assayed in the presence of urea, H protein has a pI of approximately 5.4, coat protein has a pI of approximately 4.9. Proteinase K-treated TMV RNA and H-protein-free TMV coat protein were reconstituted in vitro with or without H protein and the resulting virions were analyzed. A small amount of H protein reassociated with virions reconstituted in vitro (less than 10% of the amount found in native virions) and became resistant to degradation by trypsin, but such virions were no different from virions reconstituted without H protein in terms of yield of reconstituted particles or infectivity. In mixed reconstitution experiments with RNA and coat protein from strains U1 and Cc in all four possible combinations and with U1 H protein, the H protein always associated with the U1 coat protein. This demonstrated U1-H protein affinity for a specific coat protein rather than a specific RNA. It is unlikely that H protein functions in the early stages of viral infection, although the possibility of its having some other role in the life cycle of TMV remains.