Analysis of a new strain of Euphorbia mosaic virus with distinct replication specificity unveils a lineage of begomoviruses with short Rep sequences in the DNA-B intergenic region.

Josefat Gregorio-Jorge,Bernardo Bañuelos-Hernández,Oscar Moreno-Valenzuela,Artemiza Bernal-Alcocer,Gerardo R Argüello-Astorga,Angel G Alpuche-Solís,Cecilia Hernández-Zepeda,Gustavo Frías-Treviño

doi:10.1186/1743-422x-7-275

Abstract

BackgroundEuphorbia mosaic virus (EuMV) is a member of the SLCV clade, a lineage of New World begomoviruses that display distinctive features in their replication-associated protein (Rep) and virion-strand replication origin. The first entirely characterized EuMV isolate is native from Yucatan Peninsula, Mexico; subsequently, EuMV was detected in weeds and pepper plants from another region of Mexico, and partial DNA-A sequences revealed significant differences in their putative replication specificity determinants with respect to EuMV-YP. This study was aimed to investigate the replication compatibility between two EuMV isolates from the same country.ResultsA new isolate of EuMV was obtained from pepper plants collected at Jalisco, Mexico. Full-length clones of both genomic components of EuMV-Jal were biolistically inoculated into plants of three different species, which developed symptoms indistinguishable from those induced by EuMV-YP. Pseudorecombination experiments with EuMV-Jal and EuMV-YP genomic components demonstrated that these viruses do not form infectious reassortants in Nicotiana benthamiana, presumably because of Rep-iteron incompatibility. Sequence analysis of the EuMV-Jal DNA-B intergenic region (IR) led to the unexpected discovery of a 35-nt-long sequence that is identical to a segment of the rep gene in the cognate viral DNA-A. Similar short rep sequences ranging from 35- to 51-nt in length were identified in all EuMV isolates and in three distinct viruses from South America related to EuMV. These short rep sequences in the DNA-B IR are positioned downstream to a ~160-nt non-coding domain highly similar to the CP promoter of begomoviruses belonging to the SLCV clade.ConclusionsEuMV strains are not compatible in replication, indicating that this begomovirus species probably is not a replicating lineage in nature. The genomic analysis of EuMV-Jal led to the discovery of a subgroup of SLCV clade viruses that contain in the non-coding region of their DNA-B component, short rep gene sequences located downstream to a CP-promoter-like domain. This assemblage of DNA-A-related sequences within the DNA-B IR is reminiscent of polyomavirus microRNAs and could be involved in the posttranscriptional regulation of the cognate viral rep gene, an intriguing possibility that should be experimentally explored

Highlights

Euphorbia mosaic virus (EuMV) is a member of the SLCV clade, a lineage of New World begomoviruses that display distinctive features in their replication-associated protein (Rep) and virion-strand replication origin
More than 80% of the examined samples were polymerase chain reaction (PCR)-positive and sequence analyses of the amplicons revealed that the majority of the symptomatic plants were infected by begomoviruses belonging to two different species, Pepper huasteco yellow vein virus (PHYVV) and Pepper golden mosaic virus (PepGMV), which commonly infect pepper and tomato crops throughout the north and central areas of Mexico [22,23,24]
The complete sequence of the DNA-A and DNA-B genomic components of the unidentified begomovirus was obtained from overlapped PCR products derived from one pepper plant co-infected with PHYVV

Summary

Introduction

Euphorbia mosaic virus (EuMV) is a member of the SLCV clade, a lineage of New World begomoviruses that display distinctive features in their replication-associated protein (Rep) and virion-strand replication origin. The two genomic components are very different in overall nucleotide sequence, with the exception of a ~180-nt segment of the intergenic region (IR) displaying high sequence identity, termed the “common region” (CR) This region includes several repeated sequences (5 to 8-nt in length) called “iterons”, which are closely associated to a ~30-nt conserved element that has the potential to form a hairpin structure that harbors in its apex the invariant nonanucleotide 5’-TAATATTAC- 3’ [1]. Both the iterons and the conserved nonanucleotide in the hairpin element are functional targets for Rep, the virus-encoded protein that initiates the DNA replication by a rolling-circle (RCR) mechanism. Rep recognizes and binds to the iterons and subsequently introduces a nick into the invariant nonanucleotide to initiate the RCR process [11,12]

Objectives

Methods

Results

Discussion

Conclusion