Similarities between the secondary structure of satellite tobacco mosaic virus and tobamovirus RNAs

Gultyaev, Alexander P.; Batenburg, E van; Pleij, C.W.A.

doi:10.1099/0022-1317-75-10-2851

Cited by 37 publications

(33 citation statements)

References 21 publications

(24 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It is clear that further work is needed to determine unequivocally if interactions between the TMV replicase and the 3Ј-UTR are different for cis-preferential replication and replication in trans. An in vitro system, such as the one reported here, involving interactions of the 3Ј-UTR with RdRp derived from replication complexes formed in vivo on full-length TMV RNA could help to distinguish these possibilities, as well as defining the structural requirements for RdRp interactions with satellite TMV RNA, which also has a 3Ј-TLS and upstream pseudoknotted domain (similar to TMV domain 3) (22).…”

Section: Discussionmentioning

confidence: 99%

Role of the 3′ tRNA-Like Structure in Tobacco Mosaic Virus Minus-Strand RNA Synthesis by the Viral RNA-Dependent RNA Polymerase In Vitro

Osman

Hemenway

Buck

2000

J Virol

View full text Add to dashboard Cite

A template-dependent RNA polymerase has been used to determine the sequence elements in the 3 untranslated region of tobacco mosaic virus RNA that are required for promotion of minus-strand RNA synthesis and binding to the RNA polymerase in vitro. Regions which were important for minus-strand synthesis were domain D1, which is equivalent to a tRNA acceptor arm; domain D2, which is similar to a tRNA anticodon arm; an upstream domain, D3; and a central core, C, which connects domains D1, D2, and D3 and determines their relative orientations. Mutational analysis of the 3-terminal 4 nucleotides of domain D1 indicated the importance of the 3-terminal CA sequence for minus-strand synthesis, with the sequence CCCA or GGCA giving the highest transcriptional efficiency. Several double-helical regions, but not their sequences, which are essential for forming pseudoknot and/or stem-loop structures in domains D1, D2, and D3 and the central core, C, were shown to be required for high template efficiency. Also important were a bulge sequence in the D2 stem-loop and, to a lesser extent, a loop sequence in a hairpin structure in domain D1. The sequence of the 3 untranslated region upstream of domain D3 was not required for minus-strand synthesis. Template-RNA polymerase binding competition experiments showed that the highest-affinity RNA polymerase binding element region lay within a region comprising domain D2 and the central core, C, but domains D1 and D3 also bound to the RNA polymerase with lower affinity. Tobacco mosaic virus (TMV) is the type species of theTobamovirus genus of plant viruses. Its positive-sense, singlestranded RNA genome encodes four proteins (reviewed in references 3, 4, and 8). The 126-kDa protein, encoded by a 5Ј-proximal open reading frame (ORF), is translated from the genomic RNA. It has a domain in its N-terminal region with amino acid sequence motifs typical of methyltransferases, which is believed to be involved in the synthesis of the 5Ј cap structure, and a domain in its C-terminal region with sequences typical of RNA helicases. The 183-kDa protein is translated by readthrough of a stop codon at the end of the ORF for the 126-kDa protein. In addition to the two domains which it shares with the 126-kDa protein, the 183-kDa protein has a domain in its C-terminal region with amino acid sequence motifs typical of RNA-dependent RNA polymerases (RdRp). Both the 126-and 183-kDa proteins, which have been detected in isolated TMV replication complexes, are needed for efficient replication of TMV RNA. Recently a purified TMV RdRp was shown to contain a 126-kDa/183-kDa protein heterodimer (48). The role in TMV RNA replication of the excess 126-kDa protein which is produced in vivo is not known. TMV RNA also encodes a 30-kDa cell-to-cell movement protein and a 17.5-kDa capsid protein, which are translated from different 3Ј-coterminal subgenomic mRNAs.Replication of TMV RNA takes place in two stages: synthesis of a minus strand using the virus plus-strand RNA as a template is followed by synthesis of progeny ...

show abstract

Section: Discussionmentioning

confidence: 99%

Role of the 3′ tRNA-Like Structure in Tobacco Mosaic Virus Minus-Strand RNA Synthesis by the Viral RNA-Dependent RNA Polymerase In Vitro

Osman

Hemenway

Buck

2000

J Virol

View full text Add to dashboard Cite

show abstract

“…For proper estimates of the parameters in the formulas, we used some sequences of known pseudoknots that are evidenced by experiments and/or phylogenetic comparisons, assuming that the free energies of these pseudoknots are lower than those of corresponding hairpins formed by the pseudoknot stems+ As seen in Table 1, these H-pseudoknots cover rather broad ranges of loop and stem sizes+ The majority of pseudoknots, available for analysis, are found in viral RNAs (ten Dam et al+, 1990;Deiman & Pleij, 1997) and representative structures are shown in Figure 2+ The large group of well-documented H-pseudoknots are found at the very 39 ends of plant viral RNAs (tymoviruses and tobamoviruses) as parts of tRNA-like structures (for review, see, e+g+, Mans et al+, 1991)+ These pseudoknots seem to have minimal loop sizes and show little variation in stem lengths, with a stem S1 of 3 bp and S2 of 4 bp in tobamoviruses and 5-6 bp in tymoviruses (Fig+ 2A)+ Upstream of the tRNA-like structure in tobamoviruses, a conserved structure of three consecutive pseudoknots is located (Fig+ 2B), which seems to be very important in regulation of viral multiplication and mRNA translation (van Belkum et al+, 1985;Leathers et al+, 1993)+ Those three pseudoknots or only two are duplicated in some tobamoviruses and satellite tobacco mosaic virus, sometimes with a considerable sequence variation (Gultyaev et al+, 1994)+ Similar pseudoknot stalks are conserved in some hordei-, furoand tobraviruses and satellite tobacco necrosis viruses STNV-1 and STNV-2 (Pleij et al+, 1986;Danthinne et al+, 1991;Solovyev et al+, 1996;Koenig et al+, 1998), with different numbers of pseudoknots (Table 1)+ The biggest variation in the sizes of pseudoknot loops and stems is observed in the sites of pseudoknot-dependent ribosomal frameshift and readthrough (ten Dam et al+, 1990;Brierley et al+, 1991;Chamorro et al+, 1992;Garcia et al+, 1993;Kujawa et al+, 1993;Wills et al+, 1994)+ Although large pseudoknot loops, like those found in frameshift sites of coronaviruses (Fig+ 2E), may have an interior structure, we included them in our analysis to test the performance of logarithmic extrapolation+ For each analyzed pseudoknot, the condition of lower free energy than that of either of two hairpins formed separately by stems S1 or S2 (Fig+ 1) leads to the requirement that the sum of loop energies be less than some computable value+ In these calculations, possible coaxial stacking on stems adjacent to the pseudoknots, as in 39-terminal tRNA-like structures or pseudoknot stalks (Fig+ 2A,B), was also taken into account+ Possible extensions of stems, when they are formed separately, were also considered+ Also, in case of...…”

Section: Estimates Of Loop Energies Using Proven Pseudoknotsmentioning

confidence: 99%

An approximation of loop free energy values of RNA H-pseudoknots

Gultyaev

Batenburg

Pleij

1999

RNA

View full text Add to dashboard Cite

show abstract

“…The natural helper for STMV is tobacco mild green mosaic virus (TMGMV), although other tobamoviruses, including TMV-U1, can act as less e¤cient helpers. The 3'-end of STMV can be folded into a tRNAlike structure and UPD (Gultyaev et al 1994), which presumably acts as a binding site for the replicase to initiate negative-strand RNA synthesis. However, this structure resembles that of the 3'-end of TMV-U1 RNA more closely than the 3'-end of the RNA of its natural helper, TMGMV (Gultyaev et al 1994).…”

Section: Cis-acting Sequences Required For Tmv Rna Replicationmentioning

confidence: 99%

“…The 3'-end of STMV can be folded into a tRNAlike structure and UPD (Gultyaev et al 1994), which presumably acts as a binding site for the replicase to initiate negative-strand RNA synthesis. However, this structure resembles that of the 3'-end of TMV-U1 RNA more closely than the 3'-end of the RNA of its natural helper, TMGMV (Gultyaev et al 1994). There is little sequence similarity between the 5'-terminal regions of STMV and those of its helpers.…”

Section: Cis-acting Sequences Required For Tmv Rna Replicationmentioning

confidence: 99%

Replication of tobacco mosaic virus RNA

Buck

1999

Phil. Trans. R. Soc. Lond. B

View full text Add to dashboard Cite

The replication of tobacco mosaic virus (TMV) RNA involves synthesis of a negative-strand RNA using the genomic positive-strand RNA as a template, followed by the synthesis of positive-strand RNA on the negative-strand RNA templates. Intermediates of replication isolated from infected cells include completely double-stranded RNA (replicative form) and partly double-stranded and partly single-stranded RNA (replicative intermediate), but it is not known whether these structures are double-stranded or largely single-stranded in vivo. The synthesis of negative strands ceases before that of positive strands, and positive and negative strands may be synthesized by two di¡erent polymerases. The genomic-length negative strand also serves as a template for the synthesis of subgenomic mRNAs for the virus movement and coat proteins. Both the virus-encoded 126-kDa protein, which has amino-acid sequence motifs typical of methyltransferases and helicases, and the 183-kDa protein, which has additional motifs characteristic of RNA-dependent RNA polymerases, are required for e¤cient TMV RNA replication. Puri¢ed TMV RNA polymerase also contains a host protein serologically related to the RNA-binding subunit of the yeast translational initiation factor, eIF3. Study of Arabidopsis mutants defective in RNA replication indicates that at least two host proteins are needed for TMV RNA replication. The tomato resistance gene Tm-1 may also encode a mutant form of a host protein component of the TMV replicase. TMV replicase complexes are located on the endoplasmic reticulum in close association with the cytoskeleton in cytoplasmic bodies called viroplasms, which mature to produce`X bodies'. Viroplasms are sites of both RNA replication and protein synthesis, and may provide compartments in which the various stages of the virus mutiplication cycle (protein synthesis, RNA replication, virus movement, encapsidation) are localized and coordinated. Membranes may also be important for the con¢guration of the replicase with respect to initiation of RNA synthesis, and synthesis and release of progeny single-stranded RNA.

show abstract

Similarities between the secondary structure of satellite tobacco mosaic virus and tobamovirus RNAs

Cited by 37 publications

References 21 publications

Role of the 3′ tRNA-Like Structure in Tobacco Mosaic Virus Minus-Strand RNA Synthesis by the Viral RNA-Dependent RNA Polymerase In Vitro

Role of the 3′ tRNA-Like Structure in Tobacco Mosaic Virus Minus-Strand RNA Synthesis by the Viral RNA-Dependent RNA Polymerase In Vitro

An approximation of loop free energy values of RNA H-pseudoknots

Replication of tobacco mosaic virus RNA

Contact Info

Product

Resources

About