Possible gene interchange between plasmid and chromosome in yeast

Utatsu, Ikuyo; Imura, Toshiaki; Toh‐e, Akio

doi:10.1002/yea.320040303

Cited by 6 publications

(2 citation statements)

References 23 publications

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“…We propose that this region was formed by the capture of plasmid and viral sequences by the same mechanism that captures mitochondrial DNA to form NUMTs (43,65). In a literature search, we could find only one previous report of a similar finding: Utatsu et al (59) reported the sequences of two regions of nuclear DNA from Zygosaccharomyces rouxii that were highly similar to parts of the 2m-like plasmid pSR1 from that species, but rearranged.…”

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confidence: 87%

Evolutionary Capture of Viral and Plasmid DNA by Yeast Nuclear Chromosomes

Frank

Wolfe

2009

Eukaryot Cell

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A 10-kb region of the nuclear genome of the yeast Vanderwaltozyma polyspora contains an unusual cluster of five pseudogenes homologous to five different genes from yeast killer viruses, killer plasmids, the 2m plasmid, and a Penicillium virus. By further database searches, we show that this phenomenon is not unique to V. polyspora but that about 40% of the sequenced genomes of Saccharomycotina species contain integrated copies of genes from DNA plasmids or RNA viruses. We propose the name NUPAVs (nuclear sequences of plasmid and viral origin) for these objects, by analogy to NUMTs (nuclear copies of mitochondrial DNA) and NUPTs (nuclear copies of plastid DNA, in plants) of organellar origin. Although most of the NUPAVs are pseudogenes, one intact and active gene that was formed in this way is the KHS1 chromosomal killer locus of Saccharomyces cerevisiae. We show that KHS1 is a NUPAV related to M2 killer virus double-stranded RNA. Many NUPAVs are located beside tRNA genes, and some contain sequences from a mixture of different extrachromosomal sources. We propose that NUPAVs are sequences that were captured by the nuclear genome during the repair of double-strand breaks that occurred during evolution and that some of their properties may be explained by repeated breakage at fragile chromosomal sites.It is well known that the nuclear genomes of most eukaryotes contain integrated fragments of organellar DNA called NUMTs (nuclear copies of mitochondrial DNA) and NUPTs (nuclear copies of plastid DNA, in plants) (26,29,44,45,57). These fragments are usually pseudogenes, although some NUMTs and NUPTs have become incorporated into functional nuclear genes (38). The NUMTs present in the nuclear genomes of Saccharomycotina yeast species were recently analyzed by Sacerdot et al. (48).In addition to their mitochondrial genomes, yeast species contain a variety of other extranuclear DNA and RNA elements, including viruses and plasmids. These extrachromosomal elements are usually considered to be autonomous entities that do not interact with nuclear DNA. When our laboratory sequenced the genome of the yeast Vanderwaltozyma polyspora (synonym: Kluyveromyces polysporus) (49), we were therefore surprised to find the genomic region we describe here, which contains integrated fragments of several plasmid-and virus-like sequences. We propose that this region was formed by the capture of plasmid and viral sequences by the same mechanism that captures mitochondrial DNA to form NUMTs (43, 65). In a literature search, we could find only one previous report of a similar finding: Utatsu et al. (59) reported the sequences of two regions of nuclear DNA from Zygosaccharomyces rouxii that were highly similar to parts of the 2m-like plasmid pSR1 from that species, but rearranged.Before describing the V. polyspora region, and similar regions found in other species, we will first briefly introduce the extrachromosomal RNA and DNA entities that are known to exist in yeasts. Extrachromosomal nucleic acids are relatively uncommon in yeasts: a broad...

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confidence: 87%

Evolutionary Capture of Viral and Plasmid DNA by Yeast Nuclear Chromosomes

Frank

Wolfe

2009

Eukaryot Cell

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“…This could occur through illegitimate recombination between the plasmid and chromosomal sequences. In this context, it is noteworthy that Utatsu et al (117) identified a gene in one strain of Z. )'oilxii, but not in others, that shows a high degree of homology to the P gene of pSR1.…”

Section: Origin Of 2um Circle-like Plasmidsmentioning

confidence: 94%

Deoxyribonucleic acid plasmids in yeasts.

Volkert¹,

Wilson²,

Broach³

1989

Microbiological Reviews

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sources for the replication and transmission of the element and not compromising the fitness of the host cell. An evaluation of the deoxyribonucleic acid (DNA) plasmid species found naturally in yeasts presents an anthology of approaches to stable, extrachromosomal persistence. In this review we describe all the DNA plasmids that have been isolated and characterized from different yeasts, focusing our attention on the mechanisms underlying their successful existence as extrachromosomal elements.

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