The Reacquisition of Biotin Prototrophy in <i>Saccharomyces cerevisiae</i> Involved Horizontal Gene Transfer, Gene Duplication and Gene Clustering

Hall, Charles R.; Dietrich, Fred S.

doi:10.1534/genetics.107.074963

Cited by 146 publications

(136 citation statements)

References 55 publications

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“…Some of these genes, like SNO/SNZ and SAM, are functionally clustered. Previous studies have shown that there are very few functionally clustered genes in S. cerevisiae, and that those that are clustered tend to be associated with specific functions that differ between strains (Hall and Dietrich 2007). Analogous distributions of nonessential genes are also found in other species.…”

Section: Discussionmentioning

confidence: 85%

Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production

Argueso

Carazzolle

Mieczkowski³

et al. 2009

Genome Res.

252

236

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Bioethanol is a biofuel produced mainly from the fermentation of carbohydrates derived from agricultural feedstocks by the yeast Saccharomyces cerevisiae. One of the most widely adopted strains is PE-2, a heterothallic diploid naturally adapted to the sugar cane fermentation process used in Brazil. Here we report the molecular genetic analysis of a PE-2 derived diploid (JAY270), and the complete genome sequence of a haploid derivative (JAY291). The JAY270 genome is highly heterozygous (;2 SNPs/kb) and has several structural polymorphisms between homologous chromosomes. These chromosomal rearrangements are confined to the peripheral regions of the chromosomes, with breakpoints within repetitive DNA sequences. Despite its complex karyotype, this diploid, when sporulated, had a high frequency of viable spores. Hybrid diploids formed by outcrossing with the laboratory strain S288c also displayed good spore viability. Thus, the rearrangements that exist near the ends of chromosomes do not impair meiosis, as they do not span regions that contain essential genes. This observation is consistent with a model in which the peripheral regions of chromosomes represent plastic domains of the genome that are free to recombine ectopically and experiment with alternative structures. We also explored features of the JAY270 and JAY291 genomes that help explain their high adaptation to industrial environments, exhibiting desirable phenotypes such as high ethanol and cell mass production and high temperature and oxidative stress tolerance. The genomic manipulation of such strains could enable the creation of a new generation of industrial organisms, ideally suited for use as delivery vehicles for future bioenergy technologies.

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Section: Discussionmentioning

confidence: 85%

Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production

Argueso

Carazzolle

Mieczkowski³

et al. 2009

Genome Res.

252

236

View full text Add to dashboard Cite

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“…Although no structural ortholog of bioF is found in S. cerevisiae, AON synthase is encoded in this organism and in closely related species by BIO6, a structural paralog of the BIO3 gene, which encodes the bacterium-type DAN synthase (12,30). Because no peroxisomal targeting sequence was identified in Bio6p, we investigated the roles of the peroxisome and ␤-oxidation cycle in S. cerevisiae biotin synthesis.…”

Section: Biotin Synthesis Requiresmentioning

confidence: 99%

“…Because no peroxisomal targeting sequence was identified in Bio6p, we investigated the roles of the peroxisome and ␤-oxidation cycle in S. cerevisiae biotin synthesis. Many S. cerevisiae laboratory strains, including reference strain BY4742 used in the Saccharomyces Genome Deletion Project, require biotin due the absence of the syntenic BIO6 and BIO1 genes (12,30). The BIO6-BIO1 gene cluster of prototrophic strain A364a was cloned and introduced into BY4742 and the deletions mutants derived from it, and all strains were tested for biotin prototrophy.…”

Section: Biotin Synthesis Requiresmentioning

confidence: 99%

Contributions of the Peroxisome and β-Oxidation Cycle to Biotin Synthesis in Fungi

Magliano

Flipphi

Arpat

et al. 2011

Journal of Biological Chemistry

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Background: Pimeloyl-CoA is an intermediate of the biotin pathway, but it is unknown how it is synthesized in fungi. Results: Aspergillus nidulans mutants in ␤-oxidation are biotin-deficient, and the enzyme utilizing pimeloyl-CoA is targeted to the peroxisome. Conclusion: Pimeloyl-CoA is synthesized in the peroxisome via the ␤-oxidation cycle in filamentous fungi. Significance: This is the first implication of peroxisomal ␤-oxidation in biotin synthesis.

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“…However, eukaryotic gene order is not as random as it first appeared, and clusters of functionally related but nonhomologous genes now have been identified in the genomes of animals and fungi (2,3). These clusters include the MHC locus in mammals (4), gene clusters for nutrient use in yeast (5)(6)(7), and numerous clusters for diverse secondary metabolic pathways in filamentous fungi (8,9). Although the genes within these eukaryotic clusters are transcribed independently, these clusters have certain operon-like features (physical clustering and coregulation) (3).…”

mentioning

confidence: 99%

Formation of plant metabolic gene clusters within dynamic chromosomal regions

Field

Fiston-Lavier

Kemen

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

216

248

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In bacteria, genes with related functions often are grouped together in operons and are cotranscribed as a single polycistronic mRNA. In eukaryotes, functionally related genes generally are scattered across the genome. Notable exceptions include gene clusters for catabolic pathways in yeast, synthesis of secondary metabolites in filamentous fungi, and the major histocompatibility complex in animals. Until quite recently it was thought that gene clusters in plants were restricted to tandem duplicates (for example, arrays of leucine-rich repeat disease-resistance genes). However, operon-like clusters of coregulated nonhomologous genes are an emerging theme in plant biology, where they may be involved in the synthesis of certain defense compounds. These clusters are unlikely to have arisen by horizontal gene transfer, and the mechanisms behind their formation are poorly understood. Previously in thale cress (Arabidopsis thaliana) we identified an operon-like gene cluster that is required for the synthesis and modification of the triterpene thalianol. Here we characterize a second operon-like triterpene cluster (the marneral cluster) from A. thaliana, compare the features of these two clusters, and investigate the evolutionary events that have led to cluster formation. We conclude that common mechanisms are likely to underlie the assembly and control of operon-like gene clusters in plants.O perons are a familiar feature of prokaryote genomes, where genes belonging to the same functional pathway are assembled into a single transcriptional unit. In eukaryotes, operons are rare [with a few notable exceptions such as in the genomes of nematodes (1)], and functionally related genes usually are scattered across the genome. However, eukaryotic gene order is not as random as it first appeared, and clusters of functionally related but nonhomologous genes now have been identified in the genomes of animals and fungi (2, 3). These clusters include the MHC locus in mammals (4), gene clusters for nutrient use in yeast (5-7), and numerous clusters for diverse secondary metabolic pathways in filamentous fungi (8,9). Although the genes within these eukaryotic clusters are transcribed independently, these clusters have certain operon-like features (physical clustering and coregulation) (3).In plants, genes for well-characterized secondary metabolic pathways such as the anthocyanin pathway are unlinked. However, the first gene cluster for a plant secondary metabolic pathway-for the synthesis of cyclic hydroxamic acids-was discovered in maize (Zea mays) in 1997 (10), and since then a secondary metabolic gene cluster for the synthesis of the triterpene avenacin has been discovered in diploid oat (Avena strigosa) (11-14), and two clusters for the synthesis of different diterpenes (momilactones and phytocassanes) have been characterized in rice (Oryza sativa) (15-18). These four clusters from cereals are all required for the synthesis of preformed or stress-induced compounds implicated in plant defense (15,16,19,20). We recently identifie...

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The Reacquisition of Biotin Prototrophy in Saccharomyces cerevisiae Involved Horizontal Gene Transfer, Gene Duplication and Gene Clustering

Cited by 146 publications

References 55 publications

Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production

Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production

Contributions of the Peroxisome and β-Oxidation Cycle to Biotin Synthesis in Fungi

Formation of plant metabolic gene clusters within dynamic chromosomal regions

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