scholarly journals Genetic Variation and Possible Mechanisms Driving the Evolution of Worldwide Fig mosaic virus Isolates

2014 ◽  
Vol 104 (1) ◽  
pp. 108-114 ◽  
Author(s):  
Jeewan Jyot Walia ◽  
Anouk Willemsen ◽  
Eminur Elci ◽  
Kadriye Caglayan ◽  
Bryce W. Falk ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Mosaic Virus ◽  
Rna Virus ◽  
Plant Viruses ◽  
Long Distance ◽  
Evolutionary Mechanisms ◽  
Plant Materials ◽  
Genomic Rnas ◽  
Fig Trees ◽  
Fig Mosaic Virus

Fig mosaic virus (FMV) is a multipartite negative-sense RNA virus infecting fig trees worldwide. FMV is transmitted by vegetative propagation and grafting of plant materials, and by the eriophyid mite Aceria ficus. In this work, the genetic variation and evolutionary mechanisms shaping FMV populations were characterized. Nucleotide sequences from four genomic regions (each within the genomic RNAs 1, 2, 3, and 4) from FMV isolates from different countries were determined and analyzed. FMV genetic variation was low, as is seen for many other plant viruses. Phylogenetic analysis showed some geographically distant FMV isolates which clustered together, suggesting long-distance migration. The extent of migration was limited, although varied, between countries, such that FMV populations of different countries were genetically differentiated. Analysis using several recombination algorithms suggests that genomes of some FMV isolates originated by reassortment of genomic RNAs from different genetically similar isolates. Comparison between nonsynonymous and synonymous substitutions showed selection acting on some amino acids; however, most evolved neutrally. This and neutrality tests together with the limited gene flow suggest that genetic drift plays an important role in shaping FMV populations.

scholarly journals Beet necrotic yellow vein virus subgenomic RNA3 is a cleavage product leading to stable non-coding RNA required for long-distance movement

2012 ◽  
Vol 93 (5) ◽  
pp. 1093-1102 ◽  
Author(s):  
Claire Peltier ◽  
Elodie Klein ◽  
Kamal Hleibieh ◽  
Massimiliano D’Alonzo ◽  
Philippe Hammann ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Rna Virus ◽  
Cleavage Product ◽  
Yellow Vein ◽  
35S Promoter ◽  
Long Distance ◽  
Non Coding Rna ◽  
Long Distance Movement

Beet necrotic yellow vein virus (BNYVV) is a multipartite RNA virus. BNYVV RNA3 does not accumulate in non-host transgenic Arabidopsis thaliana plants when expressed using a 35S promoter. However, a 3′-derivative species has been detected in transgenic plants and in transient expression assays conducted in Nicotiana benthamiana and Beta macrocarpa. The 3′-derivative species is similar to the previously reported subgenomic RNA3 produced during virus infection. 5′ RACE revealed that the truncated forms had identical 5′ ends. The 5′ termini carried the coremin motif also present on BNYVV RNA5, beet soil-borne mosaic virus RNA3 and 4, and cucumber mosaic virus group 2 RNAs. This RNA3 species lacks a m7Gppp at the 5′ end of the cleavage products, whether expressed transiently or virally. Mutagenesis revealed the importance of the coremin sequence for both long-distance movement and stabilization of the cleavage product in vivo and in vitro. The isolation of various RNA3 5′-end products suggests the existence of a cleavage between nt 212 and 1234 and subsequent exonucleolytic degradation, leading to the accumulation of a non-coding RNA. When RNA3 was incubated in wheatgerm extracts, truncated forms appeared rapidly and their appearance was protein- and divalent ion-dependent.

scholarly journals A Unique Glycine-Rich Motif at the N-terminal Region of Bamboo mosaic virus Coat Protein Is Required for Symptom Expression

2010 ◽  
Vol 23 (7) ◽  
pp. 903-914 ◽  
Author(s):  
Ping Lan ◽  
Wen-Bin Yeh ◽  
Chih-Wei Tsai ◽  
Na-Sheng Lin
Keyword(s):  
Mass Spectrometry ◽  
Mosaic Virus ◽  
Mutational Analysis ◽  
Plant Viruses ◽  
Site Directed Mutagenesis ◽  
Mass Spectrometry Analysis ◽  
Coat Proteins ◽  
Long Distance ◽  
Spectrometry Analysis ◽  
Local Lesions

The coat proteins (CP) of many plant viruses are multifunctional proteins. We used N-terminal sequencing and mass spectrometry/mass spectrometry analysis to identify a truncated form of the Bamboo mosaic virus (BaMV) CP missing the N-terminal 35 amino acids (N35). The N35 region is unique in the potexviruses by its containing a glycine-rich motif (GRM) not present in databases but highly conserved among BaMV isolates. Results from site-directed mutagenesis and deletion mutational analysis showed that loss of this region converted necrotic local lesions to chlorotic local lesions on Chenopodium quinoa leaves. Furthermore, this region is required for successful development of mosaic symptoms on Nicotiana benthamiana leaves but is dispensable for BaMV replication and cell-to-cell and long-distance movement as well as virion assembly. This unique GRM-containing region of BaMV CP may be a symptom determinant in specific hosts.

scholarly journals Identification and characterization of two novel genomic RNA segments of fig mosaic virus, RNA5 and RNA6

2012 ◽  
Vol 93 (7) ◽  
pp. 1612-1619 ◽  
Author(s):  
Kazuya Ishikawa ◽  
Kensaku Maejima ◽  
Ken Komatsu ◽  
Yugo Kitazawa ◽  
Masayoshi Hashimoto ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Rna Virus ◽  
Mosaic Disease ◽  
The Novel ◽  
Genomic Rna ◽  
Evolutionary Patterns ◽  
Rna Molecules ◽  
Fig Mosaic Virus ◽  
Identification And Characterization

Fig mosaic virus (FMV), a negative-strand RNA virus, is recognized as a causal agent of fig mosaic disease. We performed RT-PCR for 14 FMV isolates collected from symptomatic fig plants in Japan and Serbia using primers corresponding to the conserved 13 nt stretches found at the termini of FMV genomic segments. The resulting simultaneous amplification of all FMV genomic segments yielded four previously identified segments of FMV and two novel segments. These novel FMV genomic RNA segments were found in each of the 14 FMV isolates analysed. In Northern blot studies, both the sense and antisense strands of these novel RNA molecules accumulated in FMV-infected fig leaves but not in uninfected fig leaves, confirming that they replicate as FMV genomic segments. Sequence analysis showed that the novel RNA segments are similar, in their structural organization and molecular evolutionary patterns, to those of known FMV genomic RNA segments. Our findings thus indicate that these newly discovered RNA segments are previously unidentified FMV genomic segments, which we have designated RNA5 and RNA6.

scholarly journals Molecular and biological characterization of an isolate of Tomato mottle mosaic virus (ToMMV) infecting tomato and other experimental hosts in a greenhouse in Valencia, Spain

2016 ◽  
Author(s):  
S. Ambrós ◽  
F. Martínez ◽  
P. Ivars ◽  
C. Hernández ◽  
F. de la Iglesia ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Plant Species ◽  
Rna Virus ◽  
Diagnostic Techniques ◽  
Plant Viruses ◽  
Reservoir Host ◽  
Molecular Techniques ◽  
Tomato Mosaic Virus ◽  
Molecular Diagnostic ◽  
Molecular Diagnostic Techniques

AbstractTomato is known to be a natural and experimental reservoir host for many plant viruses. In the last few years a new tobamovirus species, Tomato mottle mosaic virus (ToMMV), has been described infecting tomato and pepper plants in several countries worldwide. Upon observation of symptoms in tomato plants growing in a greenhouse in Valencia, Spain, we aimed to ascertain the etiology of the disease. Using standard molecular techniques, we first detected a positive sense single-stranded RNA virus as the probable causal agent. Next, we amplified, cloned and sequenced a ~3 kb fragment of its RNA genome which allowed us to identify the virus as a new ToMMV isolate. Through extensive assays on distinct plant species, we validated Koch’s postulates and investigated the host range of the ToMMV isolate. Several plant species were locally and/or systemically infected by the virus, some of which had not been previously reported as ToMMV hosts despite they are commonly used in research greenhouses. Finally, two reliable molecular diagnostic techniques were developed and used to assess the presence of ToMMV in different plants species. We discuss the possibility that, given the high sequence homology between ToMMV and Tomato mosaic virus, the former may have been mistakenly diagnosed as the latter by serological methods.

scholarly journals Harnessing host ROS-generating machinery for the robust genome replication of a plant RNA virus

2017 ◽  
Vol 114 (7) ◽  
pp. E1282-E1290 ◽  
Author(s):  
Kiwamu Hyodo ◽  
Kenji Hashimoto ◽  
Kazuyuki Kuchitsu ◽  
Nobuhiro Suzuki ◽  
Tetsuro Okuno
Keyword(s):  
Mosaic Virus ◽  
Rna Virus ◽  
Plant Stress ◽  
Rna Replication ◽  
Plant Viruses ◽  
Brome Mosaic Virus ◽  
Viral Rna ◽  
Genome Replication ◽  
Dependent Manner ◽  
Positive Strand Rna

As sessile organisms, plants have to accommodate to rapid changes in their surrounding environment. Reactive oxygen species (ROS) act as signaling molecules to transduce biotic and abiotic stimuli into plant stress adaptations. It is established that a respiratory burst oxidase homolog B of Nicotiana benthamiana (NbRBOHB) produces ROS in response to microbe-associated molecular patterns to inhibit pathogen infection. Plant viruses are also known as causative agents of ROS induction in infected plants; however, the function of ROS in plant–virus interactions remains obscure. Here, we show that the replication of red clover necrotic mosaic virus (RCNMV), a plant positive-strand RNA [(+)RNA] virus, requires NbRBOHB-mediated ROS production. The RCNMV replication protein p27 plays a pivotal role in this process, redirecting the subcellular localization of NbRBOHB and a subgroup II calcium-dependent protein kinase of N. benthamiana (NbCDPKiso2) from the plasma membrane to the p27-containing intracellular aggregate structures. p27 also induces an intracellular ROS burst in an RBOH-dependent manner. NbCDPKiso2 was shown to be an activator of the p27-triggered ROS accumulations and to be required for RCNMV replication. Importantly, this RBOH-derived ROS is essential for robust viral RNA replication. The need for RBOH-derived ROS was demonstrated for the replication of another (+)RNA virus, brome mosaic virus, suggesting that this characteristic is true for plant (+)RNA viruses. Collectively, our findings revealed a hitherto unknown viral strategy whereby the host ROS-generating machinery is diverted for robust viral RNA replication.

scholarly journals tRNA-Like Structure Regulates Translation of Brome Mosaic Virus RNA

2004 ◽  
Vol 78 (8) ◽  
pp. 4003-4010 ◽  
Author(s):  
Sharief Barends ◽  
Joëlle Rudinger-Thirion ◽  
Catherine Florentz ◽  
Richard Giegé ◽  
Cornelis W. A. Pleij ◽  
...  
Keyword(s):  
Coat Protein ◽  
Protein Expression ◽  
Mosaic Virus ◽  
Dominant Role ◽  
Initiation Site ◽  
Plant Viruses ◽  
Brome Mosaic Virus ◽  
Trna Synthetase ◽  
Yellow Mosaic Virus ◽  
Genomic Rnas

ABSTRACT For various groups of plant viruses, the genomic RNAs end with a tRNA-like structure (TLS) instead of the 3′ poly(A) tail of common mRNAs. The actual function of these TLSs has long been enigmatic. Recently, however, it became clear that for turnip yellow mosaic virus, a tymovirus, the valylated TLSTYMV of the single genomic RNA functions as a bait for host ribosomes and directs them to the internal initiation site of translation (with N-terminal valine) of the second open reading frame for the polyprotein. This discovery prompted us to investigate whether the much larger TLSs of a different genus of viruses have a comparable function in translation. Brome mosaic virus (BMV), a bromovirus, has a tripartite RNA genome with a subgenomic RNA4 for coat protein expression. All four RNAs carry a highly conserved and bulky 3′ TLSBMV (about 200 nucleotides) with determinants for tyrosylation. We discovered TLSBMV-catalyzed self-tyrosylation of the tyrosyl-tRNA synthetase but could not clearly detect tyrosine incorporation into any virus-encoded protein. We established that BMV proteins do not need TLSBMV tyrosylation for their initiation. However, disruption of the TLSs strongly reduced the translation of genomic RNA1, RNA2, and less strongly, RNA3, whereas coat protein expression from RNA4 remained unaffected. This aberrant translation could be partially restored by providing the TLSBMV in trans. Intriguingly, a subdomain of the TLSBMV could even almost fully restore translation to the original pattern. We discuss here a model with a central and dominant role for the TLSBMV during the BMV infection cycle.

scholarly journals Domain organization of the N-terminal portion of hordeivirus movement protein TGBp1

2009 ◽  
Vol 90 (12) ◽  
pp. 3022-3032 ◽  
Author(s):  
Valentin V. Makarov ◽  
Ekaterina N. Rybakova ◽  
Alexander V. Efimov ◽  
Eugene N. Dobrov ◽  
Marina V. Serebryakova ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Molecular Mass ◽  
Rna Binding ◽  
Triple Gene Block ◽  
Plant Viruses ◽  
Protein Domain ◽  
Helicase Domain ◽  
Long Distance ◽  
Genomic Rnas ◽  
Gene Block

Three ‘triple gene block’ proteins known as TGBp1, TGBp2 and TGBp3 are required for cell-to-cell movement of plant viruses belonging to a number of genera including Hordeivirus. Hordeiviral TGBp1 interacts with viral genomic RNAs to form ribonucleoprotein (RNP) complexes competent for translocation between cells through plasmodesmata and over long distances via the phloem. Binding of hordeivirus TGBp1 to RNA involves two protein regions, the C-terminal NTPase/helicase domain and the N-terminal extension region. This study demonstrated that the extension region of hordeivirus TGBp1 consists of two structurally and functionally distinct domains called the N-terminal domain (NTD) and the internal domain (ID). In agreement with secondary structure predictions, analysis of circular dichroism spectra of the isolated NTD and ID demonstrated that the NTD represents a natively unfolded protein domain, whereas the ID has a pronounced secondary structure. Both the NTD and ID were able to bind ssRNA non-specifically. However, whilst the NTD interacted with ssRNA non-cooperatively, the ID bound ssRNA in a cooperative manner. Additionally, both domains bound dsRNA. The NTD and ID formed low-molecular-mass oligomers, whereas the ID also gave rise to high-molecular-mass complexes. The isolated ID was able to interact with both the NTD and the C-terminal NTPase/helicase domain in solution. These data demonstrate that the hordeivirus TGBp1 has three RNA-binding domains and that interaction between these structural units can provide a basis for remodelling of viral RNP complexes at different steps of cell-to-cell and long-distance transport of virus infection.

scholarly journals A 1,000-Year-Old RNA Virus

2018 ◽  
Vol 93 (1) ◽  
Author(s):  
Mahtab Peyambari ◽  
Sylvia Warner ◽  
Nicholas Stoler ◽  
Drew Rainer ◽  
Marilyn J. Roossinck
Keyword(s):  
Plant Virus ◽  
Rna Virus ◽  
Plant Viruses ◽  
Persea Americana ◽  
Illumina Hiseq ◽  
Genomic Rnas ◽  
Double Stranded Rna ◽  
Complete Genomes ◽  
Complete Sequences ◽  
Maize Cobs

ABSTRACTOnly a few RNA viruses have been discovered from archaeological samples, the oldest dating from about 750 years ago. Using ancient maize cobs from Antelope house, Arizona, dating from ca. 1,000 CE, we discovered a novel plant virus with a double-stranded RNA genome. The virus is a member of the familyChrysoviridaethat infect plants and fungi in a persistent manner. The extracted double-stranded RNA from 312 maize cobs was converted to cDNA, and sequences were determined using an Illumina HiSeq 2000. Assembled contigs from many samples showed similarity toAnthuriummosaic-associated virus andPersea americanachrysovirus, putative species in theChrysovirusgenus, and nearly complete genomes were found in three ancient maize samples. We named this new virusZea mayschrysovirus 1. Using specific primers, we were able to recover sequences of a closely related virus from modern maize and obtained the nearly complete sequences of the three genomic RNAs. Comparing the nucleotide sequences of the three genomic RNAs of the modern and ancient viruses showed 98, 96.7, and 97.4% identities, respectively. Hence, in 1,000 years of maize cultivation, this virus has undergone about 3% divergence.IMPORTANCEA virus related to plant chrysoviruses was found in numerous ancient samples of maize, with nearly complete genomes in three samples. The age of the ancient samples (i.e., about 1,000 years old) was confirmed by carbon dating. Chrysoviruses are persistent plant viruses. They infect their hosts from generation to generation by transmission through seeds and can remain in their hosts for very long time periods. When modern corn samples were analyzed, a closely related chrysovirus was found with only about 3% divergence from the ancient sequences. This virus represents the oldest known plant virus.

scholarly journals Comparison by Sequence-Based and Electron Microscopic Analyses of Fig mosaic virus Isolates Obtained from Field and Experimentally Inoculated Fig Plants

Plant Disease ◽  
2010 ◽  
Vol 94 (12) ◽  
pp. 1448-1452 ◽  
Author(s):  
Kadriye Çağlayan ◽  
Çiğdem Ulubaş Serçe ◽  
Eminur Barutçu ◽  
Kamuran Kaya ◽  
Vicente Medina ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Mosaic Virus ◽  
Mosaic Disease ◽  
Electron Microscopic ◽  
Mesophyll Cells ◽  
Donor Plant ◽  
Transmission Electron ◽  
Pcr Products ◽  
Fig Trees ◽  
Fig Mosaic Virus

Fig mosaic disease (FMD) and the fig mite, Aceria ficus, are widespread in different fig growing provinces of Turkey. Fig trees (Ficus carica) cv. Bursa siyahı (D1) and an unknown seedling (D2) that showed typical FMD symptoms and was heavily infested by fig mites were used as donor plants for attempted mite transmissions to healthy fig seedlings. Transmission electron microscopy observations of donor plant samples prior to the transmission tests were performed and showed the presence of double membrane bodies (DMBs) in the palisade mesophyll cells. Electron microscopy of all experimentally inoculated fig seedlings showed the same bodies. This result reinforced the suggestion that an agent that elicits the production of DMBs in infected cells is involved in the etiology of FMD. Double-stranded (ds)RNA analyses were also performed from experimentally inoculated plants, and dsRNAs with sizes approximately 1.30 and 1.96 kb were obtained. Reverse transcription–polymerase chain reaction (RT-PCR) products of 468 and 298 bp specific to Fig mosaic virus (FMV) were amplified from both donor and experimentally inoculated plants. BLAST analyses of nucleotide sequences of these fragments showed 90% identity with FMV for the donor plant and 94 to 96% for experimentally inoculated plants. According to these results, FMV is present in both donor and experimentally inoculated plants in Turkey, and this virus is transmissible by A. ficus from fig plant to fig plant.

scholarly journals The Multifunctional Long-Distance Movement Protein of Pea Enation Mosaic Virus 2 Protects Viral and Host Transcripts from Nonsense-Mediated Decay

mBio ◽  
2020 ◽  
Vol 11 (2) ◽  
Author(s):  
Jared P. May ◽  
Philip Z. Johnson ◽  
Muhammad Ilyas ◽  
Feng Gao ◽  
Anne E. Simon
Keyword(s):  
Mosaic Virus ◽  
Rna Viruses ◽  
Rna Virus ◽  
Messenger Rnas ◽  
Rna Seq ◽  
Long Distance ◽  
Content Type ◽  
Nonsense Mediated Decay ◽  
Long Distance Movement ◽  
Pea Enation Mosaic Virus

ABSTRACT The nonsense-mediated decay (NMD) pathway presents a challenge for RNA viruses with termination codons that precede extended 3′ untranslated regions (UTRs). The umbravirus Pea enation mosaic virus 2 (PEMV2) is a nonsegmented, positive-sense RNA virus with an unusually long 3′ UTR that is susceptible to NMD. To establish a systemic infection, the PEMV2 long-distance movement protein p26 was previously shown to both stabilize viral RNAs and bind them for transport through the plant’s vascular system. The current study demonstrated that p26 protects both viral and nonviral messenger RNAs from NMD. Although p26 localizes to both the cytoplasm and nucleolus, p26 exerts its anti-NMD effects exclusively in the cytoplasm independently of long-distance movement. Using a transcriptome-wide approach in the model plant Nicotiana benthamiana, p26 protected a subset of cellular NMD target transcripts, particularly those containing long, structured, GC-rich 3′ UTRs. Furthermore, transcriptome sequencing (RNA-seq) revealed that the NMD pathway is highly dysfunctional during PEMV2 infection, with 1,820 (48%) of NMD targets increasing in abundance. Widespread changes in the host transcriptome are common during plant RNA virus infections, and these results suggest that, in at least some instances, virus-mediated NMD inhibition may be a major contributing factor. IMPORTANCE Nonsense-mediated decay (NMD) represents an RNA regulatory pathway that degrades both natural and faulty messenger RNAs with long 3′ untranslated regions. NMD targets diverse families of RNA viruses, requiring that viruses counteract the NMD pathway for successful amplification in host cells. A protein required for long-distance movement of Pea enation mosaic virus 2 (PEMV2) is shown to also protect both viral and host mRNAs from NMD. RNA-seq analyses of the Nicotiana benthamiana transcriptome revealed that PEMV2 infection significantly impairs the host NMD pathway. RNA viruses routinely induce large-scale changes in host gene expression, and, like PEMV2, may use NMD inhibition to alter the host transcriptome in an effort to increase virus amplification.

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