The genome of Beet cryptic virus 1 shows high homology to certain cryptoviruses present in phylogenetically distant hosts

Szegő, Anita; Enünlü, Natalya; Deshmukh, S. D.; Veliceasa, Dorina; Hunyadi‐Gulyás, Éva; Kühne, Thomas D.; Ilyés, Pál; Potyondi, L.; Medzihradszky, Katalin F.; Lukàcs, Noèmi

doi:10.1007/s11262-009-0432-4

Cited by 20 publications

(11 citation statements)

References 43 publications

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“…Within this group, PCLSs from the families Brassicaceae (BrPCLS5, BoPCLS5, and BnPCLS5) and Solanaceae (StPCLS5, SpPCLS5, SlPCLS5, and NtPCLS5-1) comprised 2 subgroups that included CPs encoded by RSCV1 (CP) and RSCV1 dsRNA3 (Figure 4), respectively, which are considered to be from two different partitiviruses. PCLS4s from members of the genus Brassica clustered together with CPs of other plant partitiviruses including white clover cryptic virus 1 (WCCV1) [32], CaCV1, beet cryptic virus 1 (BCV1) [33], and vicia cryptic virus (VCV) [34].…”

Section: Resultsmentioning

confidence: 99%

Widespread Endogenization of Genome Sequences of Non-Retroviral RNA Viruses into Plant Genomes

et al. 2011

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Non-retroviral RNA virus sequences (NRVSs) have been found in the chromosomes of vertebrates and fungi, but not plants. Here we report similarly endogenized NRVSs derived from plus-, negative-, and double-stranded RNA viruses in plant chromosomes. These sequences were found by searching public genomic sequence databases, and, importantly, most NRVSs were subsequently detected by direct molecular analyses of plant DNAs. The most widespread NRVSs were related to the coat protein (CP) genes of the family Partitiviridae which have bisegmented dsRNA genomes, and included plant- and fungus-infecting members. The CP of a novel fungal virus (Rosellinia necatrix partitivirus 2, RnPV2) had the greatest sequence similarity to Arabidopsis thaliana ILR2, which is thought to regulate the activities of the phytohormone auxin, indole-3-acetic acid (IAA). Furthermore, partitivirus CP-like sequences much more closely related to plant partitiviruses than to RnPV2 were identified in a wide range of plant species. In addition, the nucleocapsid protein genes of cytorhabdoviruses and varicosaviruses were found in species of over 9 plant families, including Brassicaceae and Solanaceae. A replicase-like sequence of a betaflexivirus was identified in the cucumber genome. The pattern of occurrence of NRVSs and the phylogenetic analyses of NRVSs and related viruses indicate that multiple independent integrations into many plant lineages may have occurred. For example, one of the NRVSs was retained in Ar. thaliana but not in Ar. lyrata or other related Camelina species, whereas another NRVS displayed the reverse pattern. Our study has shown that single- and double-stranded RNA viral sequences are widespread in plant genomes, and shows the potential of genome integrated NRVSs to contribute to resolve unclear phylogenetic relationships of plant species.

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Section: Resultsmentioning

confidence: 99%

Widespread Endogenization of Genome Sequences of Non-Retroviral RNA Viruses into Plant Genomes

et al. 2011

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“…A nucleotide sequence alignment was generated using all the RdRp sequences determined during the present study, the HaV, Heterobasidion parviporum partitivirus Fr110B, as well as two representatives of closely related virus strains from hosts other than Heterobasidion: the Amasya Cherry Disease (ACD)-associated mycovirus (Coutts et al 2004) and the Beet cryptic virus 1 (Szego et al 2010). The nucleotide sequences were translated after the removal of 5 0 and 3 0 untranslated regions (UTR's) and aligned manually based on initial MAFFT and ClustalW alignments.…”

Section: Bioinformatics and Phylogenetic Analysismentioning

confidence: 99%

Species of Heterobasidion host a diverse pool of partitiviruses with global distribution and interspecies transmission

et al. 2011

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“…To the resins 100 µl of Laemmli sample buffer were added, boiled and 20 µl aliquots were loaded onto a 10% SDS-PAGE gel, electrophoresed and stained with colloidal Coomassie Brillant Blue [64]. Selected protein bands were cut out, the proteins were reduced, alkylated and in-gel digested with trypsin as described earlier [65]. The tryptic digests were analyzed by LC-MS/MS using an LCQ Fleet 3D ion trap mass spectrometer (Thermo Fischer Scientific) in a data-dependent fashion, in triple-play mode.…”

Section: Methodsmentioning

confidence: 99%

“…Proteins represented by at least 2 unique sequences with a score>40, i.e. with p<0.05, are reported [65]. The same, eluted protein fractions were also analyzed by immuno-blotting, using the following specific antibodies: h PARP-1 (Santa Cruz; sc-7150, H250), h Topoisomerase I (Topogen; 2012-1).…”

Section: Methodsmentioning

confidence: 99%

The Guanine-Quadruplex Structure in the Human c-myc Gene's Promoter Is Converted into B-DNA Form by the Human Poly(ADP-Ribose)Polymerase-1

et al. 2012

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The important regulatory role of the guanine-quadruplex (GQ) structure, present in the nuclease hypersensitive element (NHE) III1 region of the human c-myc (h c-myc) gene's promoter, in the regulation of the transcription of that gene has been documented. Here we present evidences, that the human nuclear poly(ADP-ribose)polymerase-1 (h PARP-1) protein participates in the regulation of the h c-myc gene expression through its interaction with this GQ structure, characterized by binding assays, fluorescence energy transfer (FRET) experiments and by affinity pull-down experiments in vitro, and by chromatin immunoprecipitation (ChIP)-qPCR analysis and h c-myc-promoter-luciferase reporter determinations in vivo. We surmise that h PARP-1 binds to the GQ structure and participates in the conversion of that structure into the transcriptionally more active B-DNA form. The first Zn-finger structure present in h PARP-1 participates in this interaction. PARP-1 might be a new member of the group of proteins participating in the regulation of transcription through their interactions with GQ structures present in the promoters of different genes.

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The genome of Beet cryptic virus 1 shows high homology to certain cryptoviruses present in phylogenetically distant hosts

Abstract: The online version of this article (doi:10.1007/s11262-009-0432-4) contains supplementary material, which is available to authorized users.

Cited by 20 publications

References 43 publications

Widespread Endogenization of Genome Sequences of Non-Retroviral RNA Viruses into Plant Genomes

Widespread Endogenization of Genome Sequences of Non-Retroviral RNA Viruses into Plant Genomes

Species of Heterobasidion host a diverse pool of partitiviruses with global distribution and interspecies transmission

The Guanine-Quadruplex Structure in the Human c-myc Gene's Promoter Is Converted into B-DNA Form by the Human Poly(ADP-Ribose)Polymerase-1

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