Beta vulgaris mitovirus 1 in diverse cultivars of beet and chard.

Recent results indicate that mitoviruses, which replicate persistently in host mitochondria, are not restricted to fungi, but instead are found also in plants. Beta vulgaris mitovirus 1 (BevuMV1) is an example first discovered in sugar beet cultivars. For the current study, complete coding sequences of 42 BevuMV1 strains were newly determined, derived from not only sugar beet but also fodder beet, table beet, and Swiss chard cultivars of Beta vulgaris, as well as wild sea beet. BevuMV1 is thus a common phytobiome component of this valuable crop species. Most of the new BevuMV1 sequences originated from RNA extracted from B. vulgaris seed clusters, consistent with vertical transmission of this virus. Results suggest that BevuMV1 entered the B. vulgaris lineage prior to human cultivation and also provides a marker for tracing the maternal ancestry of B. vulgaris cultivars. Especially notable is the monophyletic relationship and limited sequence divergence among BevuMV1 strains from cultivars that are thought or shown to share the "Owen" trait for cytoplasmic male sterility, which is transmitted by maternal mitochondria and has been broadly established in commercial breeding lines of B. vulgaris since the mid-20th century.

Evidence for contemporary plant mitoviruses.

Mitoviruses have small RNA(+) genomes, replicate in mitochondria, and have been shown to infect only fungi to date. For this report, sequences that appear to represent nearly complete plant mitovirus genomes were recovered from publicly available transcriptome data. Twenty of the refined sequences, 2684-2898 nt long and derived from 10 different species of land plants, appear to encompass the complete coding regions of contemporary plant mitoviruses, which furthermore constitute a monophyletic cluster within genus Mitovirus. Complete coding sequences of several of these viruses were recovered from multiple transcriptome (but not genome) studies of the same plant species and also from multiple plant tissues. Crop plants among implicated hosts include beet and hemp. Other new results suggest that such genuine plant mitoviruses were immediate ancestors to endogenized mitovirus elements now widespread in land plant genomes. Whether these mitoviruses are wholly cryptic with regard to plant health remains to be investigated.

Complete cryspovirus genome sequences from Cryptosporidium parvum isolate Iowa.

Bisegmented dsRNA viruses that infect most or all isolates of apicomplexan parasite Cryptosporidium parvum are currently assigned to a single species, Cryptosporidium parvum virus 1, in genus Cryspovirus, family Partitiviridae. An analysis of existing sequence data suggested that the complete sequences of both cryspovirus genome segments, dsRNA1 and dsRNA2, had yet to be determined. We therefore set out to accomplish this for the virus strain that infects C. parvum isolate Iowa. The results suggest that several previous cryspovirus sequences are indeed truncated at one or both segment termini and also identify sequences at or near the termini that are conserved in both segments. Complete sequences of other cryspovirus strains, including ones from other Cryptosporidium species, are needed for refining their classification into one or more virus species.

Nucleotide sequence of Zygosaccharomyces bailii virus Z: Evidence for +1 programmed ribosomal frameshifting and for assignment to family Amalgaviridae.

Zygosaccharomyces bailii virus Z (ZbV-Z) is a monosegmented dsRNA virus that infects the yeast Zygosaccharomyces bailii and remains unclassified to date despite its discovery >20years ago. The previously reported nucleotide sequence of ZbV-Z (GenBank AF224490) encompasses two nonoverlapping long ORFs: upstream ORF1 encoding the putative coat protein and downstream ORF2 encoding the RNA-dependent RNA polymerase (RdRp). The lack of overlap between these ORFs raises the question of how the downstream ORF is translated. After examining the previous sequence of ZbV-Z, we predicted that it contains at least one sequencing error to explain the nonoverlapping ORFs, and hence we redetermined the nucleotide sequence of ZbV-Z, derived from the same isolate of Z. bailii as previously studied, to address this prediction. The key finding from our new sequence, which includes several insertions, deletions, and substitutions relative to the previous one, is that ORF2 in fact overlaps ORF1 in the +1 frame. Moreover, a proposed sequence motif for +1 programmed ribosomal frameshifting, previously noted in influenza A viruses, plant amalgaviruses, and others, is also present in the newly identified ORF1-ORF2 overlap region of ZbV-Z. Phylogenetic analyses provided evidence that ZbV-Z represents a distinct taxon most closely related to plant amalgaviruses (genus Amalgavirus, family Amalgaviridae). We conclude that ZbV-Z is the prototype of a new species, which we propose to assign as type species of a new genus of monosegmented dsRNA mycoviruses in family Amalgaviridae. Comparisons involving other unclassified mycoviruses with RdRps apparently related to those of plant amalgaviruses, and having either mono- or bisegmented dsRNA genomes, are also discussed.

Development of recombinant Aleuria aurantia lectins with altered binding specificities to fucosylated glycans.

Changes in glycosylation have long been associated with disease. While there are many methods to detect changes in glycosylation, plant derived lectins are often used to determine changes on specific proteins or molecules of interest. One change in glycosylation that has been observed by us and by others is a disease or antigen associated increase in fucosylation on N-linked glycans. To measure this change, the fucose binding Aleuria aurantia lectin (AAL) is often utilized in plate and solution based assays. AAL is a mushroom derived lectin that contains five fucose binding sites that preferentially bind fucose linked (α-1,3, α-1,2, α-,4, and α-1,6) to N-acetyllactosamine related structures. Recently, several reports by us and by others have indicated that specific fucose linkages found on certain serum biomarker glycoprotein's are more associated with disease than others. Taking a site-directed mutagenesis approach, we have created a set of recombinant AAL proteins that display altered binding affinities to different analytes containing various fucose linkages.