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Article ; Online: Beet Curly Top Iran Virus

Ebrahimi, Saeideh / Eini, Omid / Baßler, Alexandra / Hanke, Arvid / Yildirim, Zeynep / Wassenegger, Michael / Krczal, Gabi / Uslu, Veli Vural

Viruses

2023 Volume 15, Issue 10

Abstract: Beet curly top Iran ... ...

Abstract	Beet curly top Iran virus
MeSH term(s)	RNA Interference ; Beta vulgaris ; Viral Proteins/genetics ; Viral Proteins/metabolism ; Iran ; Geminiviridae ; Nicotiana ; Plant Diseases
Chemical Substances	Viral Proteins
Language	English
Publishing date	2023-09-26
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15101996
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Article: High-Pressure-Sprayed Double Stranded RNA Does Not Induce RNA Interference of a Reporter Gene.

Uslu, Veli Vural / Bassler, Alexandra / Krczal, Gabi / Wassenegger, Michael

Frontiers in plant science

2020 Volume 11, Page(s) 534391

Abstract: In plants, RNA interference (RNAi) is an effective defense mechanism against pathogens and pests. RNAi mainly involves the micro RNA and the small interfering RNA (siRNA) pathways. The latter pathway is generally based on the processing of long double ... ...

Abstract	In plants, RNA interference (RNAi) is an effective defense mechanism against pathogens and pests. RNAi mainly involves the micro RNA and the small interfering RNA (siRNA) pathways. The latter pathway is generally based on the processing of long double stranded RNAs (dsRNA) into siRNAs by DICER-LIKE endonucleases (DCLs). SiRNAs are loaded onto ARGONAUTE proteins to constitute the RNA-induced silencing complex (RISC). Natural dsRNAs derive from transcription of inverted repeats or of specific RNA molecules that are transcribed by RNA-directed RNA polymerase 6 (RDR6). Moreover, replication of infecting viruses/viroids results in the production of dsRNA intermediates that can serve as substrates for DCLs. The high effectiveness of RNAi both locally and systemically implicated that plants could become resistant to pathogens, including viruses, through artificial activation of RNAi by topical exogenous application of dsRNA. The most preferable procedure to exploit RNAi would be to simply spray naked dsRNAs onto mature plants that are specific for the attacking pathogens serving as a substitute for pesticides applications. However, the plant cell wall is a difficult barrier to overcome and only few reports claim that topical application of naked dsRNA triggers RNAi in plants. Using a transgenic
Language	English
Publishing date	2020-12-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2020.534391
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Article ; Online: Transient expression of intron-containing transgenes generates non-spliced aberrant pre-mRNAs that are processed into siRNAs.

Dalakouras, Athanasios / Lauter, Anja / Bassler, Alexandra / Krczal, Gabi / Wassenegger, Michael

Planta

2018 Volume 249, Issue 2, Page(s) 457–468

Abstract: Main conclusion: In this study, we show that aberrant pre-mRNAs from non-spliced and non-polyadenylated intron-containing transgenes are channelled to the RNA silencing pathway. In plants, improperly processed transcripts are called aberrant RNAs (ab- ... ...

Abstract	Main conclusion: In this study, we show that aberrant pre-mRNAs from non-spliced and non-polyadenylated intron-containing transgenes are channelled to the RNA silencing pathway. In plants, improperly processed transcripts are called aberrant RNAs (ab-RNAs) and are eliminated by either RNA silencing or RNA decay mechanisms. Ab-RNAs transcribed from intronless genes are copied by RNA-directed RNA polymerases (RDRs) into double-stranded RNAs which are subsequently cleaved by DICER-LIKE endonucleases into small RNAs (sRNAs). In contrast, ab-RNAs from intron-containing genes are suggested to be channelled post-splicing to exonucleolytic degradation. Yet, it is not clear how non-spliced aberrant pre-mRNAs are eliminated. We reasoned that transient expression of agroinfiltrated intron-containing transgenes in Nicotiana benthamiana would allow us to study the steady-state levels of non-spliced pre-mRNAs. SRNA deep sequencing of the agroinfiltrated transgenes revealed the presence of sRNAs mapping to the entire non-spliced pre-mRNA suggesting that RDRs (most likely RDR6) processed aberrant non-spliced pre-mRNAs. Primary and secondary sRNAs with lengths of 18-25 nucleotides (nt) were detected, with the most prominent sRNA size class of 22 nt. SRNAs also mapped to the terminator sequence, indicating that RDR substrates also comprised read-through transcripts devoid of polyadenylation tail. Importantly, the occurring sRNAs efficiently targeted cognate mRNA for degradation but failed to cleave the non-spliced pre-mRNA, corroborating the notion that sRNAs are not triggering RNA cleavage in the nucleus.
MeSH term(s)	Blotting, Northern ; Genes, Plant/genetics ; Introns/genetics ; RNA Precursors/genetics ; RNA Precursors/metabolism ; RNA Splicing ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism ; Sequence Analysis, RNA ; Nicotiana/genetics ; Nicotiana/metabolism ; Transgenes/genetics
Chemical Substances	RNA Precursors ; RNA, Small Interfering
Language	English
Publishing date	2018-09-24
Publishing country	Germany
Document type	Journal Article
ZDB-ID	208909-9
ISSN	1432-2048 ; 0032-0935 ; 1866-2749
ISSN (online)	1432-2048
ISSN	0032-0935 ; 1866-2749
DOI	10.1007/s00425-018-3015-6
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Article ; Online: Mapping of the exchangeable and dispensable domains of the RNA 2-encoded 2A(HP) protein of arabis mosaic nepovirus.

Nourinejhad Zarghani, Shaheen / Dupuis-Maguiraga, Laurence / Bassler, Alexandra / Wetzel, Thierry

Virology

2014 Volume 458-459, Page(s) 106–113

Abstract: The N-terminal domains of the RNA 2-encoded 2A(HP) proteins of the arabis mosaic (ArMV) and grapevine fanleaf (GFLV) nepoviruses were shown to be highly variable and a hotspot for intra- and inter-species recombination events. Chimeric ArMV-NW clones in ... ...

Abstract	The N-terminal domains of the RNA 2-encoded 2A(HP) proteins of the arabis mosaic (ArMV) and grapevine fanleaf (GFLV) nepoviruses were shown to be highly variable and a hotspot for intra- and inter-species recombination events. Chimeric ArMV-NW clones in which the N-terminal domain of 2A(HP) or the entire 2A(HP) of GFLV isolates replaced the corresponding domains of ArMV retained their infectivity, showing that the 2A(HP) proteins of ArMV-NW and GFLV are exchangeable. ArMN-NW clones with deletions of the N-terminal, core, or C-terminal domains of the ArMV-NW 2A(HP) were infectious in Chenopodium quinoa although viral RNA (especially RNA 2) accumulated at reduced levels. In contrast, deletion of the entire 2A(HP) protein or of the C-terminal two thirds of the protein abolished infectivity of the ArMV-NW clones. These results suggest that multiple functional domains are distributed throughout the 2A(HP) protein and are essential for the accumulation of viral RNA 2.
MeSH term(s)	Amino Acid Sequence ; Cloning, Molecular ; Gene Deletion ; Gene Expression Regulation, Viral/physiology ; Molecular Sequence Data ; Mosaic Viruses/genetics ; Mosaic Viruses/metabolism ; Nepovirus/genetics ; Nepovirus/metabolism ; Phylogeny ; RNA, Viral/metabolism ; Viral Proteins/genetics ; Viral Proteins/metabolism
Chemical Substances	RNA, Viral ; Viral Proteins
Language	English
Publishing date	2014-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	200425-2
ISSN	1096-0341 ; 0042-6822
ISSN (online)	1096-0341
ISSN	0042-6822
DOI	10.1016/j.virol.2014.04.025
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Article: Delivery of Hairpin RNAs and Small RNAs Into Woody and Herbaceous Plants by Trunk Injection and Petiole Absorption.

Dalakouras, Athanasios / Jarausch, Wolfgang / Buchholz, Guenther / Bassler, Alexandra / Braun, Mario / Manthey, Thorsten / Krczal, Gabi / Wassenegger, Michael

Frontiers in plant science

2018 Volume 9, Page(s) 1253

Abstract: Since its discovery, RNA interference has been widely used in crop protection. Recently, transgene-free procedures that were based on exogenous application of RNA molecules having the capacity to trigger ... ...

Abstract	Since its discovery, RNA interference has been widely used in crop protection. Recently, transgene-free procedures that were based on exogenous application of RNA molecules having the capacity to trigger RNAi
Language	English
Publishing date	2018-08-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2711035-7
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2018.01253
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Article ; Online: Replicating Potato spindle tuber viroid mediates de novo methylation of an intronic viroid sequence but no cleavage of the corresponding pre-mRNA.

Dalakouras, Athanasios / Dadami, Elena / Bassler, Alexandra / Zwiebel, Michele / Krczal, Gabi / Wassenegger, Michael

RNA biology

2015 Volume 12, Issue 3, Page(s) 268–275

Abstract: In plants, Potato spindle tuber viroid (PSTVd) replication triggers post-transcriptional gene silencing (PTGS) and RNA-directed DNA methylation (RdDM) of homologous RNA and DNA sequences, respectively. PTGS predominantly occurs in the cytoplasm, but ... ...

Abstract	In plants, Potato spindle tuber viroid (PSTVd) replication triggers post-transcriptional gene silencing (PTGS) and RNA-directed DNA methylation (RdDM) of homologous RNA and DNA sequences, respectively. PTGS predominantly occurs in the cytoplasm, but nuclear PTGS has been also reported. In this study, we investigated whether the nuclear replicating PSTVd is able to trigger nuclear PTGS. Transgenic tobacco plants carrying cytoplasmic and nuclear PTGS sensor constructs were PSTVd-infected resulting in the generation of abundant PSTVd-derived small interfering RNAs (vd-siRNAs). Northern blot analysis revealed that, in contrast to the cytoplasmic sensor, the nuclear sensor transcript was not targeted for RNA degradation. Bisulfite sequencing analysis showed that the nuclear PTGS sensor transgene was efficiently targeted for RdDM. Our data suggest that PSTVd fails to trigger nuclear PTGS, and that RdDM and nuclear PTGS are not necessarily coupled.
MeSH term(s)	Base Sequence ; Cell Nucleus/genetics ; Cell Nucleus/metabolism ; Cell Nucleus/virology ; Cytoplasm/genetics ; Cytoplasm/metabolism ; Cytoplasm/virology ; DNA Methylation ; Introns ; Molecular Sequence Data ; Plant Cells/virology ; Plant Tubers/virology ; Plants, Genetically Modified/virology ; RNA Editing ; RNA Precursors/genetics ; RNA Precursors/metabolism ; RNA, Small Interfering/biosynthesis ; RNA, Small Interfering/genetics ; RNA, Viral/genetics ; RNA, Viral/metabolism ; Solanum tuberosum/virology ; Nicotiana/virology ; Viroids/genetics ; Viroids/metabolism ; Virus Replication/genetics
Chemical Substances	RNA Precursors ; RNA, Small Interfering ; RNA, Viral
Language	English
Publishing date	2015-03-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2159587-2
ISSN	1555-8584 ; 1555-8584
ISSN (online)	1555-8584
ISSN	1555-8584
DOI	10.1080/15476286.2015.1017216
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Article: In vitro and in vivo evidence for differences in the protease activity of two arabis mosaic nepovirus isolates and their impact on the infectivity of chimeric cDNA clones

Wetzel, Thierry / Chisholm, Joan / Dupuis-Maguiraga, Laurence / Bassler, Alexandra / Sanfacon, Hélène

Virology. 2013 Nov., v. 446, no. 1-2

2013

Abstract: Regulated processing of nepovirus polyproteins allows the release of mature proteins and intermediate polyproteins. Infectious cDNA clones of the mild NW isolate of arabis mosaic virus (ArMV) and chimeric clones incorporating RNA1 segments of Lv, a ... ...

Abstract	Regulated processing of nepovirus polyproteins allows the release of mature proteins and intermediate polyproteins. Infectious cDNA clones of the mild NW isolate of arabis mosaic virus (ArMV) and chimeric clones incorporating RNA1 segments of Lv, a severe isolate, were generated. Clones containing the Lv X2–NTB cleavage site were not infectious unless the Lv protease was present. The Lv and NW X2–NTB cleavage sites differ at positions P6, P4 and P2. In vitro, processing at the X2–NTB site was undetectable or reduced in chimeric polyproteins containing the Lv X2–NTB site and the NW protease but was restored when both the Lv protease and X2–NTB site were present. In contrast, cleavage at this site was increased in polyproteins that contained the NW X2–NTB site and the Lv protease. These results show that the ArMV-Lv protease has greater activity and is active on a greater range of cleavage sites than that of ArMV-NW.
Keywords	Arabis mosaic virus ; clones ; complementary DNA ; enzyme activity ; pathogenicity ; proteinases ; proteins
Language	English
Dates of publication	2013-11
Size	p. 102-111.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	200425-2
ISSN	1096-0341 ; 0042-6822
ISSN (online)	1096-0341
ISSN	0042-6822
DOI	10.1016/j.virol.2013.07.040
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Article: Characterization of proteinase cleavage sites in the N-terminal region of the RNA1-encoded polyprotein from Arabis mosaic virus (subgroup A nepovirus).

Wetzel, Thierry / Chisholm, Joan / Bassler, Alexandra / Sanfaçon, Hélène

Virology

2008 Volume 375, Issue 1, Page(s) 159–169

Abstract: Arabis mosaic virus is a subgroup A nepovirus. The RNA1-encoded polyprotein (P1) contains the domains for the NTP-binding protein (NTB), VPg, proteinase (Pro) and polymerase at its C-terminus. Putative cleavage sites delineating these domains have been ... ...

Abstract	Arabis mosaic virus is a subgroup A nepovirus. The RNA1-encoded polyprotein (P1) contains the domains for the NTP-binding protein (NTB), VPg, proteinase (Pro) and polymerase at its C-terminus. Putative cleavage sites delineating these domains have been proposed. However, the number and location of cleavage sites upstream of the NTB domain are not known. Using in vitro processing assays, we have confirmed proteolytic cleavage at the NTB-VPg and VPg-Pro sites. In addition, we have identified two cleavage sites in the N-terminal region of P1. Site-directed mutagenesis and immunoprecipitation experiments using inserted peptide tags confirmed that the position of these cleavage sites corresponds to that of cleavage sites delineating the X1 and X2 domains in Tomato ringspot virus (subgroup C nepovirus). Amino acid alignments implied the presence of similar cleavage sites in the P1 polyprotein of other nepoviruses. Our results suggest that the presence of two protein domains upstream of NTB is a common feature of nepoviruses.
MeSH term(s)	Amino Acid Sequence ; Amino Acid Substitution/genetics ; Arabis ; Immunoprecipitation ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Nepovirus/physiology ; Peptide Hydrolases/metabolism ; Polyproteins/chemistry ; Polyproteins/metabolism ; Protein Structure, Tertiary ; Sequence Alignment ; Viral Proteins/chemistry ; Viral Proteins/metabolism
Chemical Substances	Polyproteins ; Viral Proteins ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2008-05-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	200425-2
ISSN	1096-0341 ; 0042-6822
ISSN (online)	1096-0341
ISSN	0042-6822
DOI	10.1016/j.virol.2008.01.046
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Article ; Online: In vitro and in vivo evidence for differences in the protease activity of two arabis mosaic nepovirus isolates and their impact on the infectivity of chimeric cDNA clones.

Wetzel, Thierry / Chisholm, Joan / Dupuis-Maguiraga, Laurence / Bassler, Alexandra / Sanfacon, Hélène

Virology

2013 Volume 446, Issue 1-2, Page(s) 102–111

Abstract	Regulated processing of nepovirus polyproteins allows the release of mature proteins and intermediate polyproteins. Infectious cDNA clones of the mild NW isolate of arabis mosaic virus (ArMV) and chimeric clones incorporating RNA1 segments of Lv, a severe isolate, were generated. Clones containing the Lv X2-NTB cleavage site were not infectious unless the Lv protease was present. The Lv and NW X2-NTB cleavage sites differ at positions P6, P4 and P2. In vitro, processing at the X2-NTB site was undetectable or reduced in chimeric polyproteins containing the Lv X2-NTB site and the NW protease but was restored when both the Lv protease and X2-NTB site were present. In contrast, cleavage at this site was increased in polyproteins that contained the NW X2-NTB site and the Lv protease. These results show that the ArMV-Lv protease has greater activity and is active on a greater range of cleavage sites than that of ArMV-NW.
MeSH term(s)	Arabis/virology ; DNA, Complementary ; Molecular Sequence Data ; Nepovirus/enzymology ; Nepovirus/genetics ; Nepovirus/isolation & purification ; Nepovirus/physiology ; Peptide Hydrolases/genetics ; Peptide Hydrolases/metabolism ; Protein Processing, Post-Translational ; RNA, Viral/genetics ; Recombination, Genetic ; Sequence Analysis, DNA ; Virus Replication
Chemical Substances	DNA, Complementary ; RNA, Viral ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2013-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	200425-2
ISSN	1096-0341 ; 0042-6822
ISSN (online)	1096-0341
ISSN	0042-6822
DOI	10.1016/j.virol.2013.07.040
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Article ; Online: Real-time multiplex RT-PCR for the simultaneous detection of the five main grapevine viruses.

López-Fabuel, Irene / Wetzel, Thierry / Bertolini, Edson / Bassler, Alexandra / Vidal, Eduardo / Torres, Luis B / Yuste, Alberto / Olmos, Antonio

Journal of virological methods

2013 Volume 188, Issue 1-2, Page(s) 21–24

Abstract: A real-time multiplex RT-PCR has been developed for the simultaneous detection and identification of the major RNA viruses that infect grapevines (Grapevine fanleaf virus, Arabis mosaic virus, Grapevine leafroll-associated virus 1, Grapevine leafroll- ... ...

Abstract	A real-time multiplex RT-PCR has been developed for the simultaneous detection and identification of the major RNA viruses that infect grapevines (Grapevine fanleaf virus, Arabis mosaic virus, Grapevine leafroll-associated virus 1, Grapevine leafroll-associated virus 3 and Grapevine fleck virus). Serial dilutions of infected plant extracts were tested using the new method, and the results were compared with those obtained using a commercially available ELISA and real-time singleplex RT-PCR. The two real-time RT-PCR versions detected up to the same level of dilution and were at least 10,000 times more sensitive than the ELISA. In addition, 158 grapevine plants collected in a survey of the Protected Designation of Origin in Alicante, Spain were compared using the three methods. The results of the molecular methods were very similar, with only four discordant results, and both were able to detect many more infected plants than the ELISA. The high prevalence of Grapevine fleck virus, Grapevine leafroll-associated virus 3 and Grapevine fanleaf virus suggests that the main pathways of viral introduction are infected plant material that has escaped controls and/or uncontrolled traffic of propagating plant material. Real-time multiplex RT-PCR could be used to facilitate a better control of grapevine viruses.
MeSH term(s)	Closteroviridae/classification ; Closteroviridae/genetics ; Closteroviridae/isolation & purification ; Multiplex Polymerase Chain Reaction/methods ; Nepovirus/classification ; Nepovirus/genetics ; Nepovirus/isolation & purification ; Plant Diseases/virology ; Reverse Transcriptase Polymerase Chain Reaction/methods ; Sensitivity and Specificity ; Spain ; Tymoviridae/classification ; Tymoviridae/genetics ; Tymoviridae/isolation & purification ; Virology/methods ; Vitis/virology
Language	English
Publishing date	2013-03
Publishing country	Netherlands
Document type	Comparative Study ; Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	8013-5
ISSN	1879-0984 ; 0166-0934
ISSN (online)	1879-0984
ISSN	0166-0934
DOI	10.1016/j.jviromet.2012.11.034
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