A novel subviral agent associated with a geminivirus: The first report of a DNA satellite

Abstract

Numerous plant RNA viruses have associated with them satellite (sat) RNAs that have little or no nucleotide sequence similarity to either the viral or host genomes but are completely dependent on the helper virus for replication. We report here on the discovery of a 682-nt circular DNA satellite associated with tomato leaf curl geminivirus (TLCV) infection in northern Australia. This is the first demonstration that satellite molecules are not limited to RNA viral systems. The DNA satellite (TLCV sat-DNA) is strictly dependent for replication on the helper virus replication-associated protein and is encapsidated by TLCV coat protein. It has no significant open reading frames, and it shows no significant sequence similarity to the 2766-nt helpervirus genome except for two short motifs present in separate putative stem-loop structures: TAATATTAC, which is universally conserved in all geminiviruses, and AATCGGTGTC, which is identical to a putative replication-associated protein binding motif in TLCV. Replication of TLCV sat-DNA is also supported by other taxonomically distinct geminiviruses, including tomato yellow leaf curl virus, African cassava mosaic virus, and beet curly top virus. Therefore, this unique DNA satellite does not appear to strictly conform with the requirements that dictate the specificity of interaction of geminiviral replication-associated proteins with their cognate origins as predicted by the current model of geminivirus replication.

Replication promiscuity of DNA-β satellites associated with monopartite begomoviruses; deletion mutagenesis of the Ageratum yellow vein virus DNA-β satellite localizes sequences involved in replication

“…Sequence comparison shows that this region aligns with that part of the ToLCV sat-DNA (Dry et al, 1997) containing an inverted repeat flanking a sequence that is identical to the ToLCV iteron. Mutagenesis and protein binding assays have demonstrated that this motif in both ToLCV and sat-DNA represents a high affinity Rep binding site, although it is not required for replication of either the begomovirus or its satellite (Lin et al, 2003).…”

“…Li et al (2007) recently demonstrated that approximately the 386 nt upstream of the stem-loop structure in ToLCV sat-DNA, as well as the stem-loop structure itself, are essential for replication. This includes the predicted stem-loop structure encompassing the ToLCV iteron described above (Dry et al, 1997;Lin et al, 2003). Hence, in many respects, the DNA-b replication origin resembles the multiple domains of bipartite begomoviruses (Argüello-Astorga et al, 1994;Argüello-Astorga & Ruiz-Medrano, 2001), although the specificity of Rep recognition seems more relaxed.…”

“…In contrast, the ability of intact and defective DNA-b satellites to be trans-replicated by distinct begomoviruses (Dry et al, 1997;Saunders et al, 2002;Mansoor et al, 2003) indicates that productive origin recognition is more relaxed for the satellite. Here, we have used infectious clones of AYVV, cotton leaf curl Multan virus (CLCuMV), Eupatorium yellow vein virus (EpYVV) and honeysuckle yellow vein virus (HYVV), together with their associated DNA-b satellites, to examine replication compatibility between monopartite begomoviruses and satellites, and deletion mutagenesis has localized satellite sequences that are required for replication.…”

“…Many of these apparently monopartite begomoviruses are associated with a small satellite, designated DNA-b, which is essential for maintenance of the disease. Since the description of a DNA satellite, referred to as sat-DNA, associated with the monopartite begomovirus tomato leaf curl virus (ToLCV) (Dry et al, 1997) and the isolation of the first DNA-b satellite from Ageratum conyzoides plants infected with Ageratum yellow vein virus (AYVV) (Saunders et al, 2000), more than 200 satellite sequences have been established from a range of weeds, vegetable and fibre crops in Africa and Asia, reflecting their diversity and impact on agriculture throughout the Old World (Briddon & Stanley, 2006). …”

Genomic regions of tomato leaf curl virus DNA satellite required for replication and for satellite-mediated delivery of heterologous DNAs

“…1a) was produced representing deletions in all regions of the sat-DNA except for a 77 nt region (nt 641 through nt 682 to nt 35) flanking stem-loop I, which contains the conserved nonanucleotide sequence TAATATTAC essential for sat-DNA replication (Dry et al, 1997). These sat-DNA deletion constructs were co-agroinoculated, with TLCV, into whole plants (six) or leaf strips of N. benthamiana as described previously (Dry et al, 1997;Rigden et al, 1996). Fig.…”