Application of TEV Protease in Protein Production.

In many cases, the analysis of a specific protein is impeded by the inability to purify large amounts of it from a native source. Proteins of interest may be present in minute quantities and/or purification may be plagued with technical problems. Recombinant DNA methodologies have enabled researchers to circumvent some of these limitations by producing and purifying large quantities of protein in a nonnative system. Various systems and strategies have been successfully employed, depending on the specific protein of interest and the desired use of the final end product (antibody production, crystallography studies etc.). This chapter reviews some common methods for the production of recombinant fusion proteins and specifically describes a versatrle method for the removal of affinity tags from recombinant fusions using a highly purified proteinase with an unparalleled degree of specificity. This proteinase, from the genome of tobacco etch virus (TEV), demonstrates specific proteolytic activity under a wide range of parameters (salt, temperature, pH), making it an excellent choice for cleavage of fusion proteins (1,2).

Genetic and biochemical dissection of transgenic RNA-mediated virus resistance.

RNA-mediated virus resistance has been observed in transgenic plants at varying frequencies, suggesting that a nuclear requirement or other pre-condition must be met. This study was undertaken to characterize genetically transgenes that confer a highly resistant state to infection by tobacco etch virus (TEV). Transgenic tobacco line 2RC-6.13, expressing an untranslatable mRNA containing the TEV coat protein open reading frame, had three distinct transgene integration events that segregated as two linkage groups. A genetic series of plants that contained zero, one, two, or all three transgene inserts in both homozygous and heterozygous conditions was produced and examined. Genetic and biochemical data suggested that RNA-mediated virus resistance is a multigenic trait in line 2RC-6.13; three or more transgenes were necessary to establish the highly resistant state. One or two transgene copies resulted in an inducible form of resistance (i.e., recovery). Transcription rates and steady state RNA levels of the transgene-derived transcript present in different members of the genetic series supported a post-transcriptional RNA degradation process as the underlying mechanism for transgene transcript reduction and virus resistance. This degradation process appeared to initiate via cleavage of specific sites within the target RNA sequence, as determined by RNA get blot and primer extension analyses of transgene-derived mRNA from various transgenic plant lines.

RNA-mediated resistance with nonstructural genes from the tobacco etch virus genome.

Sense RNA-mediated virus resistance has been described for transgenic plants expressing potyviral capsid protein sequences. This study was undertaken to determine if expression of other viral sequences could induce this type of virus resistance. Plants showing highly resistant or 'recovery' phenotypes were generated by expressing the tobacco etch virus (TEV) 6 kDa/21 kDa reading frames. Expression of translatable or untranslatable versions of this TEV sequence produced resistant lines. Highly resistant and recovery phenotype plants expressing TEV coat protein sequences. High transcription rates with low steady-state levels of the transgene transcript generally correlated with resistance. During recovery and induction of the resistance, RNA and protein steady-state levels decreased 5- to 20-fold, while transcription of the transgene continued at a similar level. A posttranscriptional, cellular system eliminating sequences contained in the transgene transcript and viral genome would be consistent with the results.

Expression and purification of a recombinant tobacco etch virus NIa proteinase: biochemical analyses of the full-length and a naturally occurring truncated proteinase form.

The tobacco etch virus 27-kDa nuclear inclusion a (NIa) proteinase was expressed in Escherichia coli as a recombinant fusion protein containing a seven-histidine tag at the amino-terminus. Catalytically active and inactive (by virtue of a single amino acid change) forms of the proteinase were purified to homogeneity in a two-column chromatographic procedure. The active form of the proteinase was slowly converted to a lower molecular weight form, while the inactive form was not. This conversion was dilution independent and thought to be intramolecular. Isolation of the approximately 2-kDa peptide cleavage product and determination of its N-terminal amino acid sequence positioned the cleavage site 24 amino acids from the carboxy-terminus of the proteinase. A recombinant NIa proteinase lacking the C-terminal 24 amino acids was shown to possess limited activity. Kinetic analyses of cleavage of a synthetic peptide by the full-length or truncated proteinase were conducted and indicated that the Km of the truncated proteinase was approximately fourfold higher than that of the full-length form. The truncated proteinase was approximately one-twentieth as efficient in proteolysis of the test peptide substrate as the full-length form.

Transgenic plant virus resistance mediated by untranslatable sense RNAs: expression, regulation, and fate of nonessential RNAs.

Haploid leaf tissue of tobacco cultivars K326 and K149 was transformed with several transgenes containing cDNA of the potato virus Y (PVY) coat protein (CP) open reading frame (ORF). The various transgenes containing the PVY CP ORF sequence produced (1) the expected mRNA and CP product, (2) an mRNA rendered untranslatable by introduction of a stop codon immediately after the initiation codon, or (3) an antisense RNA that was untranslatable as a result of the incorrect orientation of the PVY CP ORF behind the transcriptional promoter. Homozygous doubled haploid (DH) (diploid) plants were generated, and selfed progeny from these plants were examined. Resistance was virus specific, functioning only against PVY. An inverse correlation between transgene-derived PVY transcript steady state levels and resistance was generally noted with lines expressing the untranslatable sense version of the PVY CP ORF. A collection of DH lines, derived from a single transformation event of a common haploid plant and isogenic for the PVY transgenes expressing untranslatable sense RNA, displayed different levels of PVY resistance. Lines with actively transcribed, methylated transgene sequences had low steady state levels of transgene transcript and a virus-resistant phenotype. These results are discussed within the context of sense suppression in plants.

RNA-mediated virus resistance in transgenic plants: exploitation of a cellular pathway possibly involved in RNA degradation.

Transgenic Nicotiana tabacum cv. Burley 49 plants were generated that express the 5' untranslated region of the tobacco etch potyvirus (TEV) genome ligated to a mutated version of the TEV coat protein gene sequence that rendered it untranslatable. Eight different transgenic plant lines were analyzed for transgene expression and for resistance to TEV. Three different responses were noted when the transgenic plant lines were inoculated with TEV: 1) some were highly resistant, and no virus replication occurred; 2) some were susceptible but able to recover from systemic TEV infection; and 3) some were susceptible to TEV infection. Plant tissue displaying the recovery phenotype was analyzed for virus replication and transgene expression. Recovered tissue could not be infected with TEV and had steady-state transgene RNA levels which were five- to eightfold lower than those of unchallenged transgenic plant tissue. Nuclear runoff assays suggested a post-transcriptional reduction in specific RNA levels. The highly resistant and recovery phenotypes associated with TEV challenge inoculation and the reduction of steady-state RNA levels in recovered transgenic leaf tissue may be manifestations of a common mechanism.

Distinct functions of capsid protein in assembly and movement of tobacco etch potyvirus in plants.

Tobacco etch potyvirus engineered to express the reporter protein beta-glucuronidase (TEV-GUS) was used for direct observation and quantitation of virus translocation in plants. Four TEV-GUS mutants were generated containing capsid proteins (CPs) with single amino acid substitutions (R154D and D198R), a double substitution (DR), or a deletion of part of the N-terminal domain (delta N). Each modified virus replicated as well as the parental virus in protoplasts, but was defective in cell-to-cell movement through inoculated leaves. The R154D, D198R and DR mutants were restricted essentially to single, initially infected cells. The delta N variant exhibited slow cell-to-cell movement in inoculated leaves, but was unable to move systemically due to a lack of entry into or replication in vascular-associated cells. Both cell-to-cell and systemic movement defects of each mutant were rescued in transgenic plants expressing wild-type TEV CP. Cell-to-cell movement, but not systemic movement, of the DR mutant was rescued partially in transgenic plants expressing TEV CP lacking the C-terminal domain, and in plants expressing CP from the heterologous potyvirus, potato virus Y. Despite comparable levels of accumulation of parental virus and each mutant in symptomatic tissue of TEV CP-expressing transgenic plants, virions were detected only in parental virus- and delta N mutant-infected plants, as revealed using three independent assays. These data suggest that the potyvirus CP possesses distinct, separable activities required for virion assembly, cell-to-cell movement and long-distance transport.

Analysis of transgenic tobacco plants expressing a truncated form of a potyvirus coat protein nucleotide sequence.

Transgenic Nicotiana tabacum cv. Burley 49 plants were generated which expressed a tobacco etch virus (TEV) coat protein (CP) gene construct containing a stop codon positioned at codon 147. This gene construct was expected to produce a TEV CP lacking the carboxy-terminal 118 amino acids of the full-length 264 amino acid CP. TEV CP gene transcripts of the expected size could be detected in transgenic plants but the expected truncated CP could not be detected. Ten independent transgenic lines expressing this form of the TEV CP gene were examined in detail. Two transgenic plant lines were resistant to aphid- or mechanically transmitted TEV and one line was highly resistant. Protoplasts derived from the highly resistant plant line did not support virus replication. The data suggested that the expression of this mutated form of the TEV CP gene could interfere with TEV replication and displayed features associated with RNA-mediated virus resistance.

Release of proteins and peptides from fusion proteins using a recombinant plant virus proteinase.

An improved method for the production, cleavage, and purification of fusion proteins and peptides is described. The unique aspect of this method is dependent on the use of a proteinase from tobacco etch virus (TEV). The proteinase used is a recombinant TEV proteinase produced with a polyhistidine tract positioned at the amino terminus. The proteinase recognizes a specific, extended cleavage site sequence. The peptide or protein of interest is purified as a fusion protein with a TEV proteinase cleavage site sequence located between it and an affinity carrier portion of the fusion. Incubation with the recombinant TEV proteinase mediates release of the peptide or protein of interest. Use of the recombinant TEV proteinase to cleave fusion proteins is an improvement over use of other proteinases for several reasons, including its high degree of specificity, its insensitivity to many proteinase inhibitors generally used in protein purification, and the ready separation of both the affinity tag and the proteinase from the cleaved product of interest.

Induction of a Highly Specific Antiviral State in Transgenic Plants: Implications for Regulation of Gene Expression and Virus Resistance.

Transgenic tobacco plants expressing either a full-length form of the tobacco etch virus (TEV) coat protein or a form truncated at the N terminus of the TEV coat protein were initially susceptible to TEV infection, and typical systemic symptoms developed. However, 3 to 5 weeks after a TEV infection was established, transgenic plants "recovered" from the TEV infection, and new stem and leaf tissue emerged symptom and virus free. A TEV-resistant state was induced in the recovered tissue. The resistance was virus specific. Recovered plant tissue could not be infected with TEV, but was susceptible to the closely related virus, potato virus Y. The resistance phenotype was functional at the single-cell level because protoplasts from recovered transgenic tissue did not support TEV replication. Surprisingly, steady state transgene mRNA levels in recovered tissue were 12-to 22-fold less than transgene mRNA levels in uninoculated transgenic tissue of the same developmental stage. However, nuclear run-off studies suggested that transgene transcription rates in recovered and uninoculated plants were similar. We propose that the resistant state and reduced steady state levels of transgene transcript accumulation are mediated at the cellular level by a cytoplasmic activity that targets specific RNA sequences for inactivation.

Expression of virus-encoded proteinases: functional and structural similarities with cellular enzymes.

Many viruses express their genome, or part of their genome, initially as a polyprotein precursor that undergoes proteolytic processing. Molecular genetic analyses of viral gene expression have revealed that many of these processing events are mediated by virus-encoded proteinases. Biochemical activity studies and structural analyses of these viral enzymes reveal that they have remarkable similarities to cellular proteinases. However, the viral proteinases have evolved unique features that permit them to function in a cellular environment. In this article, the current status of plant and animal virus proteinases is described along with their role in the viral replication cycle. The reactions catalyzed by viral proteinases are not simple enzyme-substrate interactions; rather, the processing steps are highly regulated, are coordinated with other viral processes, and frequently involve the participation of other factors.

Untranslatable transcripts of the tobacco etch virus coat protein gene sequence can interfere with tobacco etch virus replication in transgenic plants and protoplasts.

Transgenic tobacco plants which express untranslatable sense or antisense forms of the tobacco etch virus potyvirus (TEV) coat protein (CP) gene sequence have been generated. One of seven transgenic plant lines expressing a CP gene antisense transcript showed an attenuation of symptoms when inoculated with TEV. Three of ten transgenic plant lines expressing untranslatable sense transcripts did not develop symptoms when inoculated with TEV. These lines were resistant to either aphid or mechanically transmitted TEV. In contrast to CP-mediated resistance reported for other viruses, resistance was (1) mediated by an RNA molecule; (2) TEV-specific (i.e., "broad-spectrum resistance" was not observed); (3) independent of inoculum levels; (4) not dependent on plant size and; (5) due to decreased levels of virus replication. Protoplast experiments were used to demonstrate that resistant plant lines did not support the production of virus protein and progeny virus at wild-type levels.

Autocatalytic activity of the tobacco etch virus NIa proteinase in viral and foreign protein sequences.

The small nuclear inclusion (NIa) protein of the tobacco etch virus (TEV) is synthesized initially as part of a genome-derived high M(r) precursor. The NIa protein releases itself from this genome-derived precursor by self-cleavage, or an autocatalytic processing event. Cleavage between specific glutamine-glycine dipeptides at the N and C termini generates the 430 amino acid or 49,000 M(r) (49K) NIa protein. The requirements of this autocatalytic release, or cis cleavage, were examined by constructing gene cassettes encoding the TEV NIa protein which could be ligated into particular locations in cDNA of the TEV genome and also into foreign gene DNA sequences. Using cell-free transcription and translation systems, polyproteins containing TEV NIa sequences were synthesized and assayed for (i) autocatalysis and (ii) the ability of a functional NIa proteinase, purified from plant tissue, to cleave in bimolecular or trans reactions various artificial polyproteins which contained an inactive form of the NIa proteinase. The NIa self-cleavage events required an active proteinase sequence and a consensus TEV cleavage site sequence at the N and C termini. These results were consistent for NIa protein sequences placed at a foreign TEV cleavage site or in unrelated proteins. Differences were noted in the trans cleavage of these sites.

Pathogen-derived resistance to a potyvirus: immune and resistant phenotypes in transgenic tobacco expressing altered forms of a potyvirus coat protein nucleotide sequence.

Transgenic Nicotiana tabacum 'Burley 49' plants containing one of six different forms of the tobacco etch virus (TEV) coat protein (CP) nucleotide sequence have been generated. In whole plant studies, R1 and R2 progeny were inoculated mechanically with TEV, and the appearance and severity of symptoms were recorded. Symptom phenotype was altered, ranging from near wild type susceptibility to apparent immunity. Protoplasts derived from wild type and transgenic Burley 49 plant lines were transfected with TEV RNA. Protoplasts from transgenic plants expressing full-length or truncated forms of TEV CP supported virus replication. Protoplasts from certain transgenic plants, producing plus- or minus-sense CP transcripts but no CP, did not support virus replication at wild type levels. A model is proposed to account for these observations.

Cleavage profiles of tobacco etch virus (TEV)-derived substrates mediated by precursor and processed forms of the TEV NIa proteinase.

Nucleotide sequences coding for proteins containing the tobacco etch virus (TEV) NIa proteinase were generated by polymerase chain reaction amplification and/or site-directed mutagenesis. These coding regions contained sequences for the proteinase alone or as part of higher Mr precursors. Following transcription and translation of these sequences in a cell-free system, the various polyproteins, all containing an active small nuclear inclusion protein (NIa) proteinase, were used to process a TEV substrate series. Most substrates were processed in a similar fashion by all proteolytic forms. However, one substrate which contained the TEV 50K/71K protein junction was differently processed by several of the polyproteins containing NIa proteinase. Substrates which previously had no identified TEV NIa proteinase cleavage sites also were tested and were not cleaved by any of the proteinase-containing polyprotein forms.

Post-translational processing of the tobacco etch virus 49-kDa small nuclear inclusion polyprotein: identification of an internal cleavage site and delimitation of VPg and proteinase domains.

The 49,000-dalton (49-kDa) small nuclear inclusion (NI) protein of tobacco etch virus (TEV) has two distinct functions associated with it. An N-terminal segment is covalently attached to the genomic length RNA and likely involved in RNA replication, while the C-terminal half is associated with a proteolytic activity critical for genome expression. The junction delineating these two proteins has not been identified. We have analyzed naturally occurring cleavage products of TEV NI proteins and have identified a possible internal cleavage site between Glu and Gly residues at TEV 49-kDa NI protein amino acids 189-190. Similar 49-kDa-derived products are formed in cell-free translation studies in minor amounts upon the addition of excess amounts of NI protein. Cleavage of the 49-kDa (430 amino acids) protein is predicted to result in the formation of two products, 21-kDa (189 amino acids) and 27 kDa (241 amino acids) in size. Complementary DNA encoding the 27-kDa C-terminal portion of the 49-kDa protein gene was cloned into various DNA sequences. This allowed us to express the 27-kDa protein alone or as part of higher molecular weight polyproteins containing flanking TEV or foreign protein sequences. This 27-kDa amino acid sequence had a proteolytic activity similar to the 49-kDa-associated activity.

Substrate recognition by the NIa proteinase of two potyviruses involves multiple domains: characterization using genetically engineered hybrid proteinase molecules.

The proteolytic activity associated with the small nuclear inclusion protein (NIa proteinase) of tobacco etch virus (TEV), a potyvirus, catalyzes several cleavages at sites within the polyprotein derived from the TEV RNA genome. The homologous proteinase of tobacco vein mottling virus (TVMV), a closely related potyvirus, cleaves at similar, yet distinct, recognition sites. We examined these proteinases, in a cell-free cleavage system, in an attempt to define the biochemical basis of substrate specificity. Each proteinase was specific for its own cleavage site sequence in cell-free trans processing reactions, and no processing of the heterologous cleavage site was evident. Domains of the proteinase which were important in determining this substrate specificity were identified by generating hybrid proteinase genes containing both TEV and TVMV NIa proteinase coding sequences. Using site-directed mutagenesis and standard recombinant DNA techniques, plasmids were constructed which contained coding sequences for hybrid TEV-TVMV proteinases. These plasmids were expressed and tested in a cell-free environment for their ability to cleave both TEV and TVMV substrates. The data suggest that the carboxy-terminal 150 amino acids of the NIa protein contain the necessary information to specifically recognize a particular cleavage site sequence, and that specificity determinants are contained in at least three interactive subdomains within this region.

Molecular genetic analyses of the soybean mosaic virus NIa proteinase.

Recombinant DNA molecules containing cDNA to a soybean mosaic virus (SMV) RNA genome were constructed and partial nucleotide sequences determined for two cDNA inserts, pSMV-34 and pSMV-35. Comparison of the predicted amino acid sequence encoded by the pSMV-34 cDNA insert to other potyvirus protein sequences revealed extensive homology with the region of the genome encoding the NIa proteinase, with conservation of the amino acids proposed to form the catalytic triad of the active site. Cell-free transcription and translation of the cloned cDNA sequence containing the NIa open reading frame and flanking sequences revealed that NIa proteinase sequences, which were expressed as part of a high Mr precursor, were able to undergo proteolytic processing. Alteration of the codon for one of the putative active site residues by site-directed mutagenesis eliminated processing and resulted in the accumulation of a high Mr precursor. Based on predicted amino acid sequences at five putative cleavage sites within the SMV polyprotein, a consensus SMV NI a proteinase cleavage sequence of Glu/Asn-Xaa-Val-Xaa-Xaa-Gln decreases Gly/Ser was proposed. The SMV NIa proteinase and its putative cleavage sites maintained motifs found in other potyviruses.

Generation and characterization of monoclonal antibodies reactive with the 49-kDa proteinase of tobacco etch virus.

Monoclonal antibodies (McAbs) were generated against two tobacco etch virus (TEV)-encoded nonstructural proteins, the 49-kilodalton (kDa) proteinase and the 58-kDa putative RNA-dependent RNA polymerase. This process was facilitated by the fact that these two TEV nonstructural proteins cocrystallize in the nuclei of virus-infected cells to form nuclear inclusion (NI) bodies which can be purified readily. The anti-NI McAbs were shown by Western blot analysis to be specific for either the TEV 49-kDa or the 58-kDa protein. Those McAbs reactive with the 49-kDa proteinase were characterized further with respect to the 49-kDa domain with which they reacted and with respect to their ability to inhibit the autocatalytic or self-processing activity of the 49-kDa proteinase. The 49-kDa antigens were synthesized from a TEV cDNA sequence using cell-free transcription and translation systems. Each anti-49-kDa McAb was used in immunoprecipitation studies with a series of 49-kDa antigens which represented a nested set of 49-kDa proteins with common amino termini but varying in length. Immunoprecipitation results showed that all of the anti-49-kDa proteinase McAbs reacted with one of five binding regions, designated A through E from the carboxy terminus of the proteinase, which were 77, 38, 81, 18, and 61 amino acids long, respectively. The 38-amino-acid binding region B contained the proposed catalytic cysteine 339 residue and was recognized by only one McAb, 4911. McAb 4911 was the only anti-49-kDa McAb capable of inhibiting the self-processing reaction in which the 49-kDa proteinase is released from its 75-kDa polyprotein precursor.

Characterization of the catalytic residues of the tobacco etch virus 49-kDa proteinase.

The 49-kDa proteinase of tobacco etch virus (TEV) cleaves the polyprotein derived from the TEV genomic RNA at five locations. Molecular genetic and biochemical analyses of the 49-kDa TEV proteinase were performed to test its homology to the cellular trypsin-like serine proteases. A cDNA fragment, containing the TEV 49-kDa proteinase gene and flanking sequences, was expressed in a cell-free transcription/translation system and resulted in the formation of a polyprotein precursor that underwent rapid self-processing. Site-directed mutagenesis was used to test the effect of altering individual 49-kDa amino acid residues on proteolysis. The data suggest that the catalytic triad of the TEV 49-kDa proteinase could be composed of the His234, Asp269, and Cys339. These findings are consistent with the hypothesis that the TEV 49-kDa proteinase is structurally similar to the trypsin-like family of serine proteinases with the substitution of Cys339 as the active site nucleophile. A structural model of the TEV 49-kDa proteinase proposes other virus-specific differences in the vicinity of the active site triad and substrate-binding pocket. The structure may explain the observed negligible effect of most cellular proteinase inhibitors on the activity of this viral proteinase.