Nanoviruses are plant viruses with a multipartite single-stranded DNA (ssDNA) genome. Alphasatellites are commonly associated with nanovirus infections, but their putative impact on their helper viruses is unknown. In this study, we investigated the role of subterranean clover stunt alphasatellite 1 (here named SCSA 1) on various important traits of (FBNYV) in its host plant and aphid vector , including disease symptoms, viral accumulation, and viral transmission. The results indicate that SCSA 1 does not affect the severity of symptoms nor overall FBNYV accumulation in , but it does change the relative amounts of its different genomic segments. Moreover, the association of SCSA 1 with FBNYV increases the rate of plant-to-plant transmission by a process seemingly unrelated to the simple increase of viral accumulation in the vector. These results represent the first study on the impact of an alphasatellite on the biology of its helper nanovirus. They suggest that SCSA 1 may benefit FBNYV, but the genericity of this conclusion is discussed and questioned. Alphasatellites are circular single-stranded DNA molecules frequently found in association with natural isolates of nanoviruses and some geminiviruses, the two ssDNA plant-infecting virus families. While the implications of alphasatellite presence in geminivirus infections are relatively well documented, comparable studies on alphasatellites associated with nanoviruses are not available. Here, we confirm that subterranean clover stunt alphasatellite 1 affects different traits of its helper nanovirus, , both in the host plant and aphid vector. We show that the frequencies of the virus segments change in the presence of alphasatellite, in both the plant and the vector. We also confirm that although within-plant virus load and symptoms are not affected by alphasatellite, the presence of alphasatellite decreases within-aphid virus load but significantly increases virus transmission rate, and thus it may confer a possible evolutionary advantage for the helper virus.
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http://dx.doi.org/10.1128/JVI.01388-21 | DOI Listing |
Nucleic Acids Res
January 2025
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
Achieving targeted hypermutation of specific genomic sequences without affecting other regions remains a key challenge in continuous evolution. To address this, we evolved a T7 RNA polymerase (RNAP) mutant that synthesizes single-stranded DNA (ssDNA) instead of RNA in vivo, while still exclusively recognizing the T7 promoter. By increasing the error rate of the T7 RNAP mutant, it generates mutated ssDNA that recombines with homologous sequences in the genome, leading to targeted genomic hypermutation.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
Single-Molecule and Cell Mechanobiology Laboratory, Daejeon, 34141, South Korea.
Helicase is a nucleic acid motor that catalyses the unwinding of double-stranded (ds) RNA and DNA via ATP hydrolysis. Helicases can act either as a nucleic acid motor that unwinds its ds substrates or as a chaperone that alters the stability of its substrates, but the two activities have not yet been reported to act simultaneously. Here, we used single-molecule techniques to unravel the synergistic coordination of helicase and chaperone activities, and found that the severe acute respiratory syndrome coronavirus helicase (nsp13) is capable of two modes of action: (i) binding of nsp13 in tandem with the fork junction of the substrate mechanically unwinds the substrate by an ATP-driven synchronous power stroke; and (ii) free nsp13, which is not bound to the substrate but complexed with ADP in solution, destabilizes the substrate through collisions between transient binding and unbinding events with unprecedented melting capability.
View Article and Find Full Text PDFThe detection of mercury ions (Hg) is crucial due to its harmful effects on health and environment. In this article, what we believe to be a novel dual-mode optical fiber sensor incorporating surface plasmon resonance (SPR) and surface-enhanced Raman scattering (SERS) is proposed for ultra-trace Hg detection. The sensing probe comprises gold (Au)/graphene oxide (GO) composite membrane structure and Au nanospheres (AuNPs), which are connected via double-stranded DNA.
View Article and Find Full Text PDFJ Chromatogr A
January 2025
Waters Corporation, Instrument/Core Research/Fundamental, Milford, MA, 01757, USA. Electronic address:
Significant progress has been made in the last two decades in producing small (<2μm), high-purity, and low-adsorption particles, columns and system hardware, for ultra-high pressure liquid chromatography (UHPLC). Simultaneously, the recent rapid expansion of cell and gene therapies for treating diseases necessitates novel analytical technologies for analyzing large (>2 kbp) plasmid double-stranded (ds) DNA (which encodes for the in vitro transcription (IVT) of single-stranded (ss) mRNA therapeutics) and dsRNAs (related to IVT production impurities) biopolymers. In this context, slalom chromatography (SC), a retention mode co-discovered in 1988, is being revitalized using the most advanced column technologies for improved determination of the critical quality attributes (CQAs) of such new therapeutics.
View Article and Find Full Text PDFBio Protoc
January 2025
International Institute of Food Innovation Co., Ltd., Nanchang University, Nanchang, China.
PCR-based genome walking is one of the prevalent techniques implemented to acquire unknown flanking genomic DNAs. The worth of genome walking includes but is not limited to cloning full-length genes, mining new genes, and discovering regulatory regions of genes. Therefore, this technique has advanced molecular biology and related fields.
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