Molecular Evolution and Phylogeny of Satellite RNA Associated with Bamboo Mosaic Potexvirus

Liu, Jih-Shiou; Hsu, Yau‐Heiu; Huang, Tzu-Lun; Lin, Na-Sheng

doi:10.1007/pl00006137

Cited by 23 publications

(29 citation statements)

References 22 publications

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“…The 5Ј UTRs of BSF4 and BSL6 satBaMVs differ in 13 nt (27). To further map the key determinant in the 5Ј UTR of BSL6, we attempted to construct chimera representing this region between the two isolates and…”

Section: Resultsmentioning

confidence: 99%

“…The two full-length infectious cDNA clones pBSF4 and pBSL6 showed a 7% difference in nucleotide sequence that dispersed in the whole molecule (27). To map the region affecting the genomic RNA replication and symptom formation by BaMV, six chimeric satellites were generated with cDNA clones derived from pBSF4 and pBSL6 by using their common BstXI and EcoNI sites at positions 159 and 652, respectively (23) (Fig.…”

Section: Resultsmentioning

confidence: 99%

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Crucial Role of the 5′ Conserved Structure ofBamboo Mosaic VirusSatellite RNA in Downregulation of Helper Viral RNA Replication

Hsu

Chen

Cheng

et al. 2006

J Virol

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Satellite RNA of Bamboo mosaic virus (satBaMV), a single-stranded mRNA type satellite encoding a protein of 20 kDa (P20), depends on the helper BaMV for replication and encapsidation. Two satBaMV isolates, BSF4 and BSL6, exhibit distinctly differential phenotypes in Nicotiana benthamiana plants when coinoculated with BaMV RNA. BSL6 significantly reduces BaMV RNA replication and suppresses the BaMV-induced symptoms, whereas BSF4 does not. By studies with chimeric satBaMVs generated by exchanging the components between BSF4 and BSL6, the genetic determinants responsible for the downregulation of BaMV replication and symptom expression were mapped at the 5 untranslated region (UTR) of BSL6. The 5 UTR of BSL6 alone is sufficient to diminish BaMV RNA replication when the 5 UTR is inserted in cis into the BaMV expression vector or when coinoculation with mutants that block the synthesis of P20 protein takes place. Further, the 5 UTR of natural satBaMV isolates contains one hypervariable (HV) region which folds into a conserved apical hairpin stem-loop ( Satellite RNAs (satRNAs) depend on their helper viruses for replication, encapsidation, and systemic movement, but they share little or no sequence similarity with the helper virus genome (reviewed in reference 38). Replication of satRNA can interfere with helper virus replication and modify the symptoms induced by the helper virus. The molecular interactions depend on the host plants, the strain of helper viruses, and the satRNA (6). For instance, some cucumber mosaic virus (CMV) satRNAs could attenuate the symptoms induced by CMV in tomato plants and others could intensify chlorotic symptoms in tomato and tobacco or necrosis in tomato (6). Sequences specifying chlorosis or necrosis were delimited to the 5Ј and/or 3Ј half of the satRNA (11, 29). The 5Ј half of minus-stranded satRNAs could induce tomato necrosis, the necrogenicity domain located in an octanucleotide loop and adjacent stem of a hairpin structure (46). Another example is the satRNA C of Turnip crinkle virus (TCV) either intensifying or attenuating symptoms, depending on the host and the level of coat protein (CP) in TCV-infected plants (16,19,39,53). Since the CP of TCV is a silencing suppressor, satRNA C can reduce the encapsidation of genomic RNA and increase the level of free CP, which implies that satRNA C may enhance TCV to overcome posttranscriptional gene silencing (47).In many cases, attenuation of symptoms is usually accompanied by a reduction in the helper virus titer (38). The attenuation associated with CMV satRNA is due to competition with the helper virus for replication by RNA-dependent RNA polymerase (RdRp) (13, 55). However, when tomato aspermy cucumovirus (TAV) was the helper virus, some satRNAs could attenuate the TAV-induced symptoms but not the level of TAV RNAs (31). Evidence also suggests that subviral RNAs can enhance the resistance of host plants (40).Bamboo mosaic virus (BaMV), a member of the potexvirus group, contains a single-stranded positive-sense RNA genome with five conse...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Crucial Role of the 5′ Conserved Structure ofBamboo Mosaic VirusSatellite RNA in Downregulation of Helper Viral RNA Replication

Hsu

Chen

Cheng

et al. 2006

J Virol

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“…9). The AAUAAA signals of virus transcripts, such as satellite RNA of bamboo mosaic potexvirus (Liu et al 1997;Cheng et al 2002;Chiu et al 2002) and CaMV 35S transcripts (Loke et al 2005), were also suggested to be located in the RNA loop. Virus is believed to produce more transcripts than host does to control host metabolism.…”

Section: Discussionmentioning

confidence: 97%

Effects of the multiple polyadenylation signal AAUAAA on mRNA 3′-end formation and gene expression

Lin

Huang

et al. 2009

Planta

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Polyadenylation (poly(A)) of eukaryotic mRNA is a critical step for gene expression. In plants, poly(A) signals leading to the formation of polyadenosine tails after mRNAs include the far upstream elements, the AAUAAA-like signals, and the mRNA cleavage sites for poly(A). Multiple AAUAAA signals leading to alternative polyadenosine formation have been found in many genes, but the effects of each AAUAAA signal on gene expression remain to be uncovered. A DNA fragment, whose transcript contains two canonical AAUAAA signals from the 3'-untranslation region of endochitinase gene of tobacco (Nicotiana tabacum L. cv. W38), was mutated and constructed into the downstream of beta-glucuronidase (GUS) coding region. Transient expression of GUS gene from these constructs indicated that the distal AAUAAA signal from the stop codon was more important than the proximal one in stimulating gene expression. Also, the sequence rather than the distance between the stop codon and the AAUAAA signal region was critical for gene expression. Transgenic tobaccos with these constructs were also generated, and the position of the polyadenosine tail formation in this region was mapped. Results revealed that both AAUAAA signals were functional, and that polyadenosine tails of most transcripts were directed by the distal AAUAAA signal. Finally, the RNA stabilities of these variants in transgenic plants were measured. RNAs from the variants with the functional distal AAUAAA signal were more stable than those with the functional proximal one only. The possible secondary structure in this poly(A) signal region was predicted and discussed.

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“…Three phylogenetic satBaMV groups were classified from natural satBaMV isolates derived from 10 infected bamboo species in different locations of Taiwan, Hainan Island of China and Delhi, India (Liu et al, 1997; Yeh et al, 2004; Wang et al, 2014). Clade I contains all other satBaMVs except most of those isolated from Ma bamboo ( Dendrocalamus latiflorus Munro) and all populations from Bambusa vulgaris .…”

Section: Bamv and Its Associated Satbamvsmentioning

confidence: 99%

“…Natural isolates of satBaMVs have been collected from BaMV-infected symptomatic bamboo plants worldwide to analyze the genetic evolution and phylogeny of satBaMVs (Liu et al, 1997; Wang et al, 2014). The mimicry of satBaMVs among the 5′- and 3′-untranslated regions (UTRs) have been investigated thoroughly (Annamalai et al, 2003; Huang et al, 2009), and the biological function of satBaMV-encoded protein elucidated its role in satBaMV replication (Lin et al, 1996), movement (Vijayapalani et al, 2006, 2012; Chang et al, 2016) and interference in BaMV replication (Hsu et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Interfering Satellite RNAs of Bamboo mosaic virus

Lin

2017

Front. Microbiol.

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Satellite RNAs (satRNAs) are sub-viral agents that may interact with their cognate helper virus (HV) and host plant synergistically and/or antagonistically. SatRNAs totally depend on the HV for replication, so satRNAs and HV usually evolve similar secondary or tertiary RNA structures that are recognized by a replication complex, although satRNAs and HV do not share an appreciable sequence homology. The satRNAs of Bamboo mosaic virus (satBaMV), the only satRNAs of the genus Potexvirus, have become one of the models of how satRNAs can modulate HV replication and virus-induced symptoms. In this review, we summarize the molecular mechanisms underlying the interaction of interfering satBaMV and BaMV. Like other satRNAs, satBaMV mimics the secondary structures of 5′- and 3′-untranslated regions (UTRs) of BaMV as a molecular pretender. However, a conserved apical hairpin stem loop (AHSL) in the 5′-UTR of satBaMV was found as the key determinant for downregulating BaMV replication. In particular, two unique nucleotides (C60 and C83) in the AHSL of satBaMVs determine the satBaMV interference ability by competing for the replication machinery. Thus, transgenic plants expressing interfering satBaMV could confer resistance to BaMV, and interfering satBaMV could be used as biological-control agent. Unlike two major anti-viral mechanisms, RNA silencing and salicylic acid-mediated immunity, our findings in plants by in vivo competition assay and RNA deep sequencing suggested replication competition is involved in this transgenic satBaMV-mediated BaMV interference. We propose how a single nucleotide of satBaMV can make a great change in BaMV pathogenicity and the underlying mechanism.

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Molecular Evolution and Phylogeny of Satellite RNA Associated with Bamboo Mosaic Potexvirus

Cited by 23 publications

References 22 publications

Crucial Role of the 5′ Conserved Structure ofBamboo Mosaic VirusSatellite RNA in Downregulation of Helper Viral RNA Replication

Crucial Role of the 5′ Conserved Structure ofBamboo Mosaic VirusSatellite RNA in Downregulation of Helper Viral RNA Replication

Effects of the multiple polyadenylation signal AAUAAA on mRNA 3′-end formation and gene expression

Interfering Satellite RNAs of Bamboo mosaic virus

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