Satellite cereal yellow dwarf virus-RPV (satRPV) RNA requires a DouXble hammerhead for self-cleavage and an alternative structure for replication 1 1Edited by D. E. Draper

Song, Sang Ik; Silver, S L; Aulik, M. A.; Rasochova, Lada; Mohan, B. R.; Miller, W. Allen

doi:10.1006/jmbi.1999.3169

Cited by 20 publications

(31 citation statements)

References 45 publications

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“…[71][72][73][74] Moreover, in the luteovirus satellite RNA, adoption of an active single-hammerhead structure in the unit-length RNA is prevented by a pseudoknot while, in oligomeric RNAs, a double-hammerhead structure lacking the pseudoknot can be formed and mediate their efficient self-cleavage. 75 Similar elements of tertiary structure (pseudoknots) have been reported in HDV ribozymes.…”

Section: ©2 0 1 1 L a N D E S B I O S C I E N C E D O N O T D I S Tsupporting

confidence: 56%

Rolling-circle replication of viroids, viroid-like satellite RNAs and hepatitis delta virus: Variations on a theme

Flores¹,

Grubb²,

Elleuch³

et al. 2011

RNA Biology

113

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Section: ©2 0 1 1 L a N D E S B I O S C I E N C E D O N O T D I S Tsupporting

confidence: 56%

Rolling-circle replication of viroids, viroid-like satellite RNAs and hepatitis delta virus: Variations on a theme

Flores¹,

Grubb²,

Elleuch³

et al. 2011

RNA Biology

113

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“…Instead, self-cleavage occurs via a doublehammerhead structure that can arise only in multimers after formation of L1-L1 and L2a-L2a helices. It was suggested that the noncleaving alternative tertiary structure is essential for some other aspect of replication than cleavage and that the L1-L2a rearrangements serve as a "riboswitch" to switch satRPV RNA between self-cleavage-competent and replication-competent conformations (43). Here we provide evidence for the overall most stable structure of the satRPV RNA monomer and the putative functions of the sequences and/or structures in satRPV RNA.…”

mentioning

confidence: 64%

“…Unlabeled, dimeric satRPV RNAs were synthesized by in vitro transcription of EcoRI-linearized templates by using T7 RNA polymerase (RiboMax kit; Promega, Madison, Wis.). To induce self-cleavage, the RNA transcripts were incubated at 37°C in cleavage buffer for approximately 3 h. satRPV transcripts were 5Ј end labeled with [␥-32 P]ATP and T4 polynucleotide kinase (40,43) on RNA previously treated with alkaline phosphatase. The labeled 322-nt monomer obtained by self-cleavage was eluted from a 6% polyacrylamide-7 M urea gel after electrophoresis and staining with ethidium bromide.…”

Section: Methodsmentioning

confidence: 99%

“…Previously it has been reported that two pentameric sequences called L1 and L2a that are loops in the functional hammerhead ribozyme of satRPV RNA can also form alternative base pairing that prevents formation of the hammerhead in the most stable predicted conformation of the monomer (43). Instead, self-cleavage occurs via a doublehammerhead structure that can arise only in multimers after formation of L1-L1 and L2a-L2a helices.…”

mentioning

confidence: 99%

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cis and trans Requirements for Rolling Circle Replication of a Satellite RNA

Song

Miller

2004

J Virol

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Satellite RNAs usurp the replication machinery of their helper viruses, even though they bear little or no sequence similarity to the helper virus RNA. In Cereal yellow dwarf polerovirus serotype RPV (CYDV-RPV), the 322-nucleotide satellite RNA (satRPV RNA) accumulates to high levels in the presence of the CYDV-RPV helper virus. Rolling circle replication generates multimeric satRPV RNAs that self-cleave via a doublehammerhead ribozyme structure. Alternative folding inhibits formation of a hammerhead in monomeric satRPV RNA. Here we determine helper virus requirements and the effects of mutations and deletions in satRPV RNA on its replication in oat cells. Using in vivo selection of a satRPV RNA pool randomized at specific bases, we found that disruption of the base pairing necessary to form the non-self-cleaving conformation reduced satRPV RNA accumulation. Unlike other satellite RNAs, both the plus and minus strands proved to be equally infectious. Accordingly, very similar essential replication structures were identified in each strand. A different region is required only for encapsidation. The CYDV-RPV RNA-dependent RNA polymerase (open reading frames 1 and 2), when expressed from the nonhelper Barley yellow dwarf luteovirus, was capable of replicating satRPV RNA. Thus, the helper virus's polymerase is the sole determinant of the ability of a virus to replicate a rolling circle satellite RNA. We present a framework for functional domains in satRPV RNA with three types of function: (i) conformational control elements comprising an RNA switch, (ii) self-functional elements (hammerhead ribozymes), and (iii) cis-acting elements that interact with viral proteins.Satellite RNAs depend on helper viruses for replication, encapsidation, and dissemination among hosts (47, 48). Satellite RNAs that form circles (circular satellite RNAs) (2,20) encode no functional open reading frames (ORFs). Thus, the helper virus and the host must provide all trans-acting factors necessary for replication. Satellite RNAs accumulate to high levels in the presence of a helper virus, despite having no sequence homology with the helper virus RNA. In contrast, viroids are autonomously replicating circular RNA pathogens that do not require a helper virus or virion (2,14,20). Circular satellite RNAs and viroids (4) are the smallest replicating nucleic acids, ranging from 225 to about 450 nucleotides (nt) in length. Thus, they serve as models for understanding the minimum requirements for the replication of genetic information. This can shed light on virus replication processes and lead to means of interfering with virus infection.Numerous studies of replication intermediates and the processing of satellite RNAs support the following rolling circle mechanism for replication of circular satellite RNAs (4, 5). Upon exiting the virion in the cell, the infectious circular plusstrand RNA is copied into a linear, multimeric minus strand (4, 5). (For satellite RNAs that encode no ORFs, we define the encapsidated strand as plus sense.) The minus stran...

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“…For these studies, the in vitro tetrameric and dimeric RNA transcripts from the template cDNAs pMBS-Tet7 and pMBS-D10, respectively, were recovered from 0.7% agarose gels by a freeze-thaw procedure as described previously (4). The purified transcripts were incubated in a buffer containing 5 mM MgCl 2 , 0.5 mM EDTA, and 50 mM Tris-HCl (pH 7.5) at 25°C for 30, 60, 90, or 120 minutes after being heated at 80°C for 1 min in 1 mM EDTA (21) or were incubated in 10 mM MgCl 2 -50 mM Tris-HCl (pH 7.5) at 37°C for the same time points, but without preheating (36). All reactions were terminated by the addition of an equal volume of 95% formamide-10 mM sodium EDTA and then immediately frozen at Ϫ80°C.…”

Section: Methodsmentioning

confidence: 99%

Analysis of Nucleotide Sequences and Multimeric Forms of a Novel Satellite RNA Associated with Beet Black Scorch Virus

Guo

Cao

et al. 2005

J Virol

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The full-length sequence of a satellite RNA (sat-RNA) of Beet black scorch virus isolate X (BBSV-X) was determined. This agent is 615 nucleotides long and lacks extensive sequence homology with its helper virus or with other reported viruses. Purified virus particles contained abundant single-stranded plus-sense monomers and smaller amounts of dimers. Single-stranded RNAs from total plant RNA extracts also included primarily monomers and smaller amounts of dimers that could be revealed by hybridization, and preparations of purified double-stranded RNAs also contained monomers and dimers. Coinoculation of in vitro transcripts of sat-RNA to Chenopodium amaranticolor with BBSV RNAs was used to assess the replication and accumulation of various forms of sat-RNA, including monomers, dimers, and tetramers. Dimeric sat-RNAs with 5-or 10-base deletions or 15-base insertions within the junction regions accumulated preferentially. In contrast, the replication of monomeric sat-RNA was severely inhibited by five-nucleotide deletions in either the 5 or the 3 termini. Therefore, sequences at both the 5 and the 3 ends of the monomers or the presence of intact juxtaposed multimers is essential for the replication of sat-RNA and for the predomination of monomeric progeny. Comparisons of the time courses of replication initiated by in vitro-synthesized monomeric or multimeric sat-RNAs raised the possibility that the dimeric form has an intermediate role in replication. We propose that replication primarily involves multimers, possibly as dimeric forms. These forms may revert to monomers by a termination of replication at 5 end sequences and/or by internal initiation at the 3 ends of multimeric junctions.Beet black scorch virus (BBSV) was first reported in the late 1980s (13,14). The virus is responsible for serious damage to the sugar beet crop in the Xinjiang, Ningxia, Inner Mongolia, Gansu, and Heilongjiang provinces of China. BBSV infects sugar beet plants systemically through the roots after transmission with Olpidium brassicae zoospores (25) and causes black scorch symptoms on the leaves (6). Mechanical inoculation in a greenhouse resulted in local infections of 15 plant species, including several Chenopodium spp., producing inapparent to extremely mild symptoms or necrotic local lesions (7). Sugar beets on different plantations contaminated by BBSV isolates in China developed similar severe black scorch symptoms on leaves, and most plants died within a week after the appearance of symptoms. Normally, only a single RNA was associated with infections, but a small single-stranded RNA (ssRNA) that is similar to the satellite RNAs (sat-RNA) of other necroviruses (39) has been found in isolates from the Xinjiang province (6). This small RNA multiplied in test plants only when associated with BBSV genomic RNA, either from the same viral isolate or from other sources of BBSV (5). The presence of sat-RNA resulted in more local lesions on the leaves of Chenopodium amaranticolor plants than did inoculation with BBSV RNA alone when the...

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Satellite cereal yellow dwarf virus-RPV (satRPV) RNA requires a DouXble hammerhead for self-cleavage and an alternative structure for replication 1 1Edited by D. E. Draper

Cited by 20 publications

References 45 publications

Rolling-circle replication of viroids, viroid-like satellite RNAs and hepatitis delta virus: Variations on a theme

Rolling-circle replication of viroids, viroid-like satellite RNAs and hepatitis delta virus: Variations on a theme

cis and trans Requirements for Rolling Circle Replication of a Satellite RNA

Analysis of Nucleotide Sequences and Multimeric Forms of a Novel Satellite RNA Associated with Beet Black Scorch Virus

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