Mapping the 5′ ends of banana bunchy top virus gene transcripts

Herrera-Valencia, Virginia Aurora; Dugdale, Benjamin; Harding, Robert M.; Dale, James L.

doi:10.1007/s00705-006-0889-6

Cited by 8 publications

(10 citation statements)

References 16 publications

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“…BBTV replicates in the nucleus via a rolling circle mechanism mediated by viral replication protein (Rep) and the host replication machinery. Each BBTV component, namely DNAs C, M, N, R, S and U3, possesses a single ORF preceded by the host RNA polymerase II (Pol II) promoter region with a TATA or TATA-like box and followed by the Pol II terminator region with a polyadenylation signal [ 14 – 16 ]. DNA-R encodes a master Rep protein mediating replication of DNA-R itself and transreplication of other components [ 14 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

A newly emerging alphasatellite affects banana bunchy top virus replication, transcription, siRNA production and transmission by aphids

et al. 2022

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Banana bunchy top virus (BBTV) is a six-component ssDNA virus (genus Babuvirus, family Nanoviridae) transmitted by aphids, infecting monocots (mainly species in the family Musaceae) and likely originating from South-East Asia where it is frequently associated with self-replicating alphasatellites. Illumina sequencing analysis of banana aphids and leaf samples from Africa revealed an alphasatellite that should be classified in a new genus, phylogenetically related to alphasatellites of nanoviruses infecting dicots. Alphasatellite DNA was encapsidated by BBTV coat protein and accumulated at high levels in plants and aphids, thereby reducing helper virus loads, altering relative abundance (formula) of viral genome components and interfering with virus transmission by aphids. BBTV and alphasatellite clones infected dicot Nicotiana benthamiana, followed by recovery and symptomless persistence of alphasatellite, and BBTV replication protein (Rep), but not alphasatellite Rep, induced leaf chlorosis. Transcriptome sequencing revealed 21, 22 and 24 nucleotide small interfering (si)RNAs covering both strands of the entire viral genome, monodirectional Pol II transcription units of viral mRNAs and pervasive transcription of each component and alphasatellite in both directions, likely generating double-stranded precursors of viral siRNAs. Consistent with the latter hypothesis, viral DNA formulas with and without alphasatellite resembled viral siRNA formulas but not mRNA formulas. Alphasatellite decreased transcription efficiency of DNA-N encoding a putative aphid transmission factor and increased relative siRNA production rates from Rep- and movement protein-encoding components. Alphasatellite itself spawned the most abundant siRNAs and had the lowest mRNA transcription rate. Collectively, following African invasion, BBTV got associated with an alphasatellite likely originating from a dicot plant and interfering with BBTV replication and transmission. Molecular analysis of virus-infected banana plants revealed new features of viral DNA transcription and siRNA biogenesis, both affected by alphasatellite. Costs and benefits of alphasatellite association with helper viruses are discussed.

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Section: Introductionmentioning

confidence: 99%

A newly emerging alphasatellite affects banana bunchy top virus replication, transcription, siRNA production and transmission by aphids

et al. 2022

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“…Another peculiar feature of these m-rep transcripts is that, among all predicted nanovirus mRNAs or mapped babuvirus transcripts (Beetham et al, 1997(Beetham et al, , 1999Herrera-Valencia et al, 2007), they have the longest 39-UTR sequences, which also comprise the IR sequences at the origin of replication. As ssDNA, the IR sequences potentially form a stem-loop structure.…”

Section: Discussionmentioning

confidence: 99%

“…Transcripts have only been mapped for BBTV (Beetham et al, 1997(Beetham et al, , 1999Herrera-Valencia et al, 2007). Transcript data for the legume-infecting nanoviruses are absent; only transcription initiation and termination signals on their respective DNAs have been recognized (Boevink et al, 1995;Katul et al, 1997;Sano et al, 1998; Shirasawa-Seo et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

“…All Rep proteins recognize the origin of replication of viral DNA (ori) and cleave it in a conserved nonamer sequence, which is flanked by inverted repeats (IRs) (Timchenko et al, 1999). This way, the Rep proteins trigger the initiation of viral positive-strand DNA synthesis, which then continues by rolling-circle replication, very similar to their action in other ssDNA viruses (Laufs et al, 1995; Timchenko et al, 1999).Transcripts have only been mapped for BBTV (Beetham et al, 1997(Beetham et al, , 1999Herrera-Valencia et al, 2007). Transcript data for the legume-infecting nanoviruses are absent; only transcription initiation and termination signals on their respective DNAs have been recognized (Boevink et al, 1995;Katul et al, 1997;Sano et al, 1998; Shirasawa-Seo et al, 2005).…”

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confidence: 99%

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Transcripts encoding the nanovirus master replication initiator proteins are terminally redundant

Grigoras

Timchenko

Gronenborn

2008

Journal of General Virology

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The multicomponent single-stranded DNA plant nanoviruses encode unique master replication initiator (Rep) proteins. We have mapped the 59 and 39 termini of the corresponding polyadenylated mRNAs from faba bean necrotic yellows virus (FBNYV) and subterranean clover stunt virus and found that these are terminally redundant by up to about 160 nt. Moreover, the origin of viral DNA replication is transcribed into RNA that is capable of folding into extended secondary structures. Other nanovirus genome components, such as the FBNYV DNA encoding the protein Clink or an FBNYV DNA encoding a non-essential para-Rep protein, are not transcribed in such a unique fashion. Thus, terminally redundant mRNAs and the resulting transcription of the replication origin appear to be restricted to nanovirus master Rep DNAs. We speculate that this may be a way to regulate the expression of the essential master Rep protein. INTRODUCTIONMembers of the family Nanoviridae comprise the species Subterranean clover stunt virus (SCSV), Faba bean necrotic yellows virus (FBNYV) and Milk vetch dwarf virus (MDV) in the genus Nanovirus, and Banana bunchy top virus (BBTV) in the genus Babuvirus (Vetten et al., 2005). The former viruses are pathogens of a wide variety of legumes in Australia (SCSV), Japan (MDV), and west Asia, north and east Africa and Spain (FBNYV), whereas BBTV only infects bananas in south Asia, the Pacific region and some African countries. The nanovirus genome consists of six to eight circular, single-stranded DNA (ssDNA) molecules of about 1 kb (Vetten et al., 2005) (Fig. 1). In general, one nanovirus DNA encodes only one protein. Common to all nanoviruses is a unique master replication initiator protein (M-Rep), encoded by DNA-R, that catalyses replication initiation and termination of its cognate and all other genome components of the respective virus (Timchenko et al., 1999Horser et al., 2001). Other genome components encode a capsid protein (DNA-S) (Chu et al., 1993;Katul et al., 1997;Wanitchakorn et al., 1997), a cellcycle link protein (Clink) (DNA-C) (Aronson et al., 2000), a movement protein (DNA-M) and a nuclear shuttle protein (DNA-N) (Wanitchakorn et al., 2000). Several DNAs encode proteins of as-yet-unknown function (DNA-U1, -U2, -U3 and -U4) (Vetten et al., 2005). Also, the biological significance of a small open reading frame (ORF) embedded completely within the m-rep gene of some BBTV isolates remains obscure (Beetham et al., 1997).In addition to these 'integral' genome components, a considerable number of non-essential DNAs, all encoding Rep proteins, were found associated with infections by all four nanoviruses (Wu et al., 1994; Vetten et al., 2005;Hu et al., 2007). These additional and non-essential rep genes can be considered as paralogues (para-rep) of the essential m-rep gene. Their precise role in the epidemiology of the nanovirus with which they associate remains unknown. However, based on the results obtained in an experimental infection system, it was suggested that the para-Repencoding DNAs may play ...

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“…The full-length sequences of all components of BBTV genome were obtained from NCBI GenBank using Taxonomy Browser till April 05, 2020 and given abbreviated names for convenience ( S1 Table ). The coding and regulatory regions, including CR-SL and CR-M were identified as described by Burns and colleagues (1995), and the sequences were started from the start of major ORF identified by Herrera-Valencia and colleagues (2007) [ 39 ] in each component for alignment through MAFFT version 6.864 [ 40 ]. The genetic diversity values of each BBTV component and subgenomic regions were determined on the aligned sequences first for Pakistani isolates and then worldwide.…”

Section: Methodsmentioning

confidence: 99%

Banana bunchy top virus genetic diversity in Pakistan and association of diversity with recombination in its genomes

Bashir

Naqvi

Muhammad³

et al. 2022

PLoS ONE

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Banana Bunchy top virus (BBTV) is a multipartite circular single strand DNA virus that belongs to genus Babuvirus and family Nanoviridae. It causes significant crop losses worldwide and also in Pakistan. BBTV is present in Pakistan since 1988 however, till now only few (about twenty only) sequence of genomic components have been reported from the country. To have insights into current genetic diversity in Pakistan fifty-seven genomic components including five complete genomes (comprises of DNA-R, -U3, -S, -M, -C and -N components) were sequenced in this study. The genetic diversity analysis of populations from Pakistan showed that DNA-R is highly conserved followed by DNA-N, whereas DNA-U3 is highly diverse with the most diverse Common Region Stem-loop (CR-SL) in BBTV genome, a functional region, which previously been reported to have undergone recombination in Pakistani population. A Maximum Likelihood (ML) phylogenetic analysis of entire genomes of isolates by using sequence of all the components concatenated together with the reported genomes around the world revealed deeper insights about the origin of the disease in Pakistan. A comparison of the genetic diversity of Pakistani and entire BBTV populations around the world indicates that there exists a correlation between genetic diversity and recombination. Population genetics analysis indicated that the degree of selection pressure differs depending on the area and genomic component. A detailed analysis of recombination across various components and functional regions suggested that recombination is closely associated with the functional parts of BBTV genome showing high genetic diversity. Both genetic diversity and recombination analyses suggest that the CR-SL is a recombination hotspot in all BBTV genomes and among the six components DNA-U3 is the only recombined component that has extensively undergone inter and intragenomic recombination. Diversity analysis of recombinant regions results on average one and half fold increase and, in some cases up to four-fold increase due to recombination. These results suggest that recombination is significantly contributing to the genetic diversity of BBTV populations around the world.

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Mapping the 5′ ends of banana bunchy top virus gene transcripts

Cited by 8 publications

References 16 publications

A newly emerging alphasatellite affects banana bunchy top virus replication, transcription, siRNA production and transmission by aphids

A newly emerging alphasatellite affects banana bunchy top virus replication, transcription, siRNA production and transmission by aphids

Transcripts encoding the nanovirus master replication initiator proteins are terminally redundant

Banana bunchy top virus genetic diversity in Pakistan and association of diversity with recombination in its genomes

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