CRUISE, a Tool for the Detection of Iterons in Circular Rep-Encoding Single-Stranded DNA Viruses.

Iterons are short, repeated DNA sequences that are important for the replication of circular single-stranded DNA viruses. No tools that can reliably predict iterons are currently available. The CRUcivirus Iteron SEarch (CRUISE) tool is a computational tool that identifies iteron candidates near stem-loop structures in viral genomes.

StemLoop-Finder: a Tool for the Detection of DNA Hairpins with Conserved Motifs.

Nucleic acid secondary structures play important roles in regulating biological processes. StemLoop-Finder is a computational tool to recognize and annotate conserved structural motifs in large data sets. The program is optimized for the detection of stem-loop structures that may serve as origins of replication in circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses.

Unveiling Crucivirus Diversity by Mining Metagenomic Data.

The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viruses that encode capsid proteins that are most closely related to those encoded by RNA viruses in the family Tombusviridae The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of capsid genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and 10 capsid-encoding circular genetic elements through de novo assembly and mining of metagenomic data. These genomes are highly diverse, as demonstrated by sequence comparisons and phylogenetic analysis of subsets of the protein sequences they encode. Most of the variation is reflected in the replication-associated protein (Rep) sequences, and much of the sequence diversity appears to be due to recombination. Our results suggest that recombination tends to occur more frequently among groups of cruciviruses with relatively similar capsid proteins and that the exchange of Rep protein domains between cruciviruses is rarer than intergenic recombination. Additionally, we suggest members of the stramenopiles/alveolates/Rhizaria supergroup as possible crucivirus hosts. Altogether, we provide a comprehensive and descriptive characterization of cruciviruses.IMPORTANCE Viruses are the most abundant biological entities on Earth. In addition to their impact on animal and plant health, viruses have important roles in ecosystem dynamics as well as in the evolution of the biosphere. Circular Rep-encoding single-stranded (CRESS) DNA viruses are ubiquitous in nature, many are agriculturally important, and they appear to have multiple origins from prokaryotic plasmids. A subset of CRESS-DNA viruses, the cruciviruses, have homologues of capsid proteins encoded by RNA viruses. The genetic structure of cruciviruses attests to the transfer of capsid genes between disparate groups of viruses. However, the evolutionary history of cruciviruses is still unclear. By collecting and analyzing cruciviral sequence data, we provide a deeper insight into the evolutionary intricacies of cruciviruses. Our results reveal an unexpected diversity of this virus group, with frequent recombination as an important determinant of variability.

Genome Sequences of Three Cruciviruses Found in the Willamette Valley (Oregon).

Cruciviruses are single-stranded DNA (ssDNA) viruses whose genomes suggest the possibility of gene transfer between DNA and RNA viruses. Many crucivirus genome sequences have been found in metagenomic data sets, although no crucivirus has been isolated. Here, we present the complete genome sequences of three cruciviruses recovered from environmental samples from Oregon.

A phage display-selected peptide inhibitor of Agrobacterium vitis polygalacturonase.

Agrobacterium vitis, the causal agent of crown gall of grapevine, is a threat to viticulture worldwide. A major virulence factor of this pathogen is polygalacturonase, an enzyme that degrades pectin components of the xylem cell wall. A single gene encodes for the polygalacturonase gene. Disruption of the polygalacturonase gene results in a mutant that is less pathogenic and produces significantly fewer root lesions on grapevines. Thus, the identification of peptides or proteins that could inhibit the activity of polygalacturonase could be part of a strategy for the protection of plants against this pathogen. A phage-displayed combinatorial peptide library was used to isolate peptides with a high binding affinity to A. vitis polygalacturonase. These peptides showed sequence similarity to regions of Oryza sativa (EMS66324, Japonica) and Triticum urartu (NP_001054402, wild wheat) polygalacturonase-inhibiting proteins (PGIPs). Furthermore, these panning experiments identified a peptide, SVTIHHLGGGS, which was able to reduce A. vitis polygalacturonase activity by 35% in vitro. Truncation studies showed that the IHHL motif alone is sufficient to inhibit A. vitis polygalacturonase activity.

Analysis of Xylem Fluid Components in Almond Cultivars Differing in Resistance to Almond Leaf Scorch Disease.

Almond leaf scorch (ALS) is caused by the pathogenic bacterium Xylella fastidiosa and poses a threat to the California almond industry. Almond cultivars are differentially resistant or susceptible to ALS. X. fastidiosa can infect but does not overwinter in resistant cultivars in sufficient numbers to cause symptoms or be detected by polymerase chain reaction. To better understand the biochemical or morphological factors mediating resistance, we extracted and analyzed almond xylem fluid from four almond cultivars differing in ALS susceptibility, including Butte and Carmel cultivars that are field resistant and Peerless and Sonora that are ALS susceptible. Xylem fluid was collected over winter months in 2007 to 2009, as well as July 2008 and April 2009, and analyzed for the following: pH, osmolarity, concentrations of sugars, calcium, magnesium, organic acids, and total phenolics. For most of these analyses, we found no clear differences in xylem fluid from resistant and susceptible almond cultivars. However, during the winter months, resistant cultivars tended to have higher concentrations of total phenolic compounds compared with susceptible cultivars (P = 0.05). In February 2009, Carmel had the highest total phenolic concentration measured, 233 µg/ml of gallic acid equivalents. The lowest phenolic concentrations occurred in April 2009. The cross-sectional areas of xylem vessels in Butte (resistant) and Peerless (susceptible) trees were not significantly different between cultivars.