Analysis of a new begomovirus unveils a composite element conserved in the CP gene promoters of several Geminiviridae genera: Clues to comprehend the complex regulation of late genes

Abstract

A novel bipartite begomovirus, Blechum interveinal chlorosis virus (BleICV), was characterized at the genome level. Comparative analyses revealed that BleICV coat protein (CP) gene promoter is highly divergent from the equivalent region of other begomoviruses (BGVs), with the single exception of Tomato chino La Paz virus (ToChLPV) with which it shares a 23-bp phylogenetic footprint exhibiting dyad symmetry. Systematic examination of the homologous CP promoter segment of 132 New World BGVs revealed the existence of a quasi-palindromic DNA segment displaying a strongly conserved ACTT-(N7)-AAGT core. The spacer sequence between the palindromic motifs is constant in length, but its sequence is highly variable among viral species, presenting a relaxed consensus (TT)GGKCCCY, which is similar to the Conserved Late Element or CLE (GTGGTCCC), a putative TrAP-responsive element. The homologous CP promoter region of Old World BGVs exhibited a distinct organization, with the putative TATA-box overlapping the left half of the ACTT-N7 composite element. Similar CP promoter sequences, dubbed “TATA-associated composite element” or TACE, were found in viruses belonging to different Geminiviridae genera, hence hinting unsuspected evolutionary relationships among those lineages. To get cues about the TACE function, the regulatory function of the CLE was explored in distinct experimental systems. Transgenic tobacco plants harboring a GUS reporter gene driven by a promoter composed by CLE multimers expressed high beta-glucuronidase activity in absence of viral factors, and that expression was increased by begomovirus infection. On the other hand, the TrAP-responsiveness of a truncated CP promoter of Tomato golden mosaic virus (TGMV) was abolished by site-directed mutation of the only CLE present in it, whereas the artificial addition of one CLE to the -125 truncated promoter strongly enhanced the transactivation level in tobacco protoplasts. These results indicate that the CLE is a TrAP-responsive element, hence providing valuable clues to interpret the recurrent association of the CLE with the TACE. On the basis of the aforesaid direct evidences and the insights afforded by the extensive comparative analysis of BleICV CP promoter, we propose that the TACE might be involved in the TrAP-mediated derepression of CP gene in vascular tissues.

High-Throughput Sequencing Reveals Differential Begomovirus Species Diversity in Non-Cultivated Plants in Northern-Pacific Mexico

“…Nonetheless, SiMSiV and RhGMV induce symptoms in their corresponding first reported hosts ( Sida rombifolia and Rhyncosia minima, respectively), with different wild species (acting as reservoirs) being suspected as the origin of the inoculum. Moreover, EuMV and EuYMV were reported previously in Euphorbia heterophylla in Mexico and Brazil [68,69]; whereas BlelCV, is a novel virus recently described in Chiapas state [70]. To the best of our knowledge, the ChiLCV, PepLRV, ToYSV, PYMV, CabLCV, SPLCV, MaBYMV, and ViYMV geminivirus-related signatures have not been previously described and/or associated to disease in Mexico and represent potential strains and/or novel viruses whose biological role needs to be determined in the immediate future.…”

Tomato Twisted Leaf Virus: A Novel Indigenous New World Monopartite Begomovirus Infecting Tomato in Venezuela

“…In ToTLV, a putative transcript from ORF 6 was suggested by RT-PCR assays (Figure 5). Besides, using the criteria to identify a putative TATA box in the CP gene promoter region of geminiviruses [35], we have identified the sequence TATTAT at the position -39 from the potential star codon, which might represent a candidate for this transcription element. However, further studies will be needed to confirm whether this potential transcript is translated and its expression might affect the viral infection.…”

Plant-virus-insect tritrophic interactions: insights into the functions of geminivirus virion-sense strand genes

“…The promoter of virion-sense strand genes contains a conserved symmetric palindromic core sequence (ACTT-N 7 -AAGT) separated by a spacer (N 7 ) sequence. Unlike the conserved GC-rich heptanucleotide spacer of 'Old World' begomoviruses, the spacer of 'New World' begomoviruses exhibited greater variability such as GGTCCCY or its variants with a single nucleotide diversity [26]. Similarly, the core sequence of Curtovirus is identified to be CCTT-N 7 -AAGG.…”

“…Moreover, deletion of cisregulatory elements i.e. GC box (of Mastrevirus) or 30 nt long CLE (of Curtovirus and Begomovirus) in the virion-sense strand promoter led to decreased promoter activity [24][25][26][27]. These cis-elements in the viral promoters probably regulate this tissue-specific gene expression.…”

“…The cis-elements encompassing CLE (5 0 -CGTCTAAGT GGTCCCGCA-3 0 ) in the viral promoter are necessary for TrAP-responsiveness of several begomoviruses [14,[26][27][28][29]. Nonetheless, CLE of all geminiviruses are not responsible for TrAP-responsiveness [30], which necessitates the identification of altered or additional TrAP-responsive elements.…”