Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis

Jeffries, Thomas W.; Grigoriev, Igor V.; Grimwood, Jane; Laplaza, José M.; Aerts, Andrea; Salamov, Asaf; Schmutz, Jeremy; Lindquist, Erika; Dehal, Paramvir; Shapiro, Harris; Liu, Jing Jing; Passoth, Volkmar; Richardson, Paul M.

doi:10.1038/nbt1290

Cited by 451 publications

(342 citation statements)

References 48 publications

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“…1 and 3) in agreement with previous phylogenetic analysis derived from concatenated mitochondrial proteins (Jung et al 2010). Conversely, the SMG phylogeny infers a sister group relationship between D. hansenii and P. stipitis in agreement with previous phylogenomic (Fitzpatrick et al 2010;Jeffries et al 2007) and phylogenetic studies (Suh et al 2006).…”

Section: Phylogenetic Relationships Among the Saccharomycotinasupporting

confidence: 80%

Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom

2011

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We have used three independent phylogenomic approaches (concatenated alignments, single-, and multigene supertrees) to reconstruct the fungal tree of life (FTOL) using publicly available fungal genomes. This is the first time multi-gene families have been used in fungal supertree reconstruction and permits us to use up to 66% of the 1,001,217 genes in our fungal database. Our analyses show that different phylogenomic datasets derived from varying clustering criteria and alignment orientation do not have a major effect on phylogenomic supertree reconstruction. Overall the resultant phylogenomic trees are relatively congruent with one another and successfully recover the major fungal phyla, subphyla and classes. We find that where incongruences do occur, the inferences are usually poorly supported. Within the Ascomycota phylum, our phylogenies reconstruct monophyletic Saccharomycotina and Pezizomycotina subphyla clades and infer a sister group relationship between these to the exclusion of the Taphrinomycotina. Within the Pezizomycotina subphylum, all three phylogenies infer a sister group relationship between the Leotiomycetes and Sordariomycetes classes. However, there is conflict regarding the relationships with the Dothideomycetes and Eurotiomycetes classes. Within the Basidiomycota phylum, supertrees derived from singleand multi-gene families infer a sister group relationship between the Pucciniomycotina and Agaricomycotina subphyla while the concatenated phylogeny infers a poorly supported relationship between the Agaricomycotina and Ustilagomycotina. The reconstruction of a robust FTOL is important for future fungal comparative analyses. We illustrate this point by performing a preliminary investigation into the phyletic distribution of yeast prion-like proteins in the fungal kingdom.

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Section: Phylogenetic Relationships Among the Saccharomycotinasupporting

confidence: 80%

Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom

2011

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“…Additional protein alignments between BY and species of the Ascomycetes phylum were performed on the SGD website by using the ''BLASTP vs. fungi'' option in the Comparison Resources drop-down menu from the Summary SGD page of the gene. The Ascomycetes species selected for these additional alignments were Schizosaccharomyces pombe (Wood et al 2002), Ashbya gossypii (Dietrich et al 2004), Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii, Yarrowia lipolytica (Dujon et al 2004), and Pichia stipitis (Jeffries et al 2007).…”

Section: Strains and Plasmidsmentioning

confidence: 99%

Polymorphisms in Multiple Genes Contribute to the Spontaneous Mitochondrial Genome Instability ofSaccharomyces cerevisiaeS288C Strains

et al. 2009

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The mitochondrial genome (mtDNA) is required for normal cellular function; inherited and somatic mutations in mtDNA lead to a variety of diseases. Saccharomyces cerevisiae has served as a model to study mtDNA integrity, in part because it can survive without mtDNA. A measure of defective mtDNA in S. cerevisiae is the formation of petite colonies. The frequency at which spontaneous petite colonies arise varies by $100-fold between laboratory and natural isolate strains. To determine the genetic basis of this difference, we applied quantitative trait locus (QTL) mapping to two strains at the opposite extremes of the phenotypic spectrum: the widely studied laboratory strain S288C and the vineyard isolate RM11-1a. Four main genetic determinants explained the phenotypic difference. Alleles of SAL1, CAT5, and MIP1 contributed to the high petite frequency of S288C and its derivatives by increasing the formation of petite colonies. By contrast, the S288C allele of MKT1 reduced the formation of petite colonies and compromised the growth of petite cells. The former three alleles were found in the EM93 strain, the founder that contributed $88% of the S288C genome. Nearly all of the phenotypic difference between S288C and RM11-1a was reconstituted by introducing the common alleles of these four genes into the S288C background. In addition to the nuclear gene contribution, the source of the mtDNA influenced its stability. These results demonstrate that a few rare genetic variants with individually small effects can have a profound phenotypic effect in combination. Moreover, the polymorphisms identified in this study open new lines of investigation into mtDNA maintenance.

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“…It is worth noting that the natural xylose-utilizing yeast S. stipitis can ferment xylose to ethanol at near the theoretical yields and produces negligible amounts of xylitol during xylose fermentation (63)(64)(65). Unlike S. stipitis, most natural xylose-fermenting yeasts produce considerable amounts of extracellular xylitol (64), and two main reasons were reported in previous studies.…”

Section: Discussionmentioning

confidence: 97%

Deletion of FPS1 , Encoding Aquaglyceroporin Fps1p, Improves Xylose Fermentation by Engineered Saccharomyces cerevisiae

Wei

Kim

et al. 2013

Appl Environ Microbiol

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Accumulation of xylitol in xylose fermentation with engineered Saccharomyces cerevisiae presents a major problem that hampers economically feasible production of biofuels from cellulosic plant biomass. In particular, substantial production of xylitol due to unbalanced redox cofactor usage by xylose reductase (XR) and xylitol dehydrogenase (XDH) leads to low yields of ethanol. While previous research focused on manipulating intracellular enzymatic reactions to improve xylose metabolism, this study demonstrated a new strategy to reduce xylitol formation and increase carbon flux toward target products by controlling the process of xylitol secretion. Using xylitol-producing S. cerevisiae strains expressing XR only, we determined the role of aquaglyceroporin Fps1p in xylitol export by characterizing extracellular and intracellular xylitol. In addition, when FPS1 was deleted in a poorly xylose-fermenting strain with unbalanced XR and XDH activities, the xylitol yield was decreased by 71% and the ethanol yield was substantially increased by nearly four times. Experiments with our optimized xylose-fermenting strain also showed that FPS1 deletion reduced xylitol production by 21% to 30% and increased ethanol yields by 3% to 10% under various fermentation conditions. Deletion of FPS1 decreased the xylose consumption rate under anaerobic conditions, but the effect was not significant in fermentation at high cell density. Deletion of FPS1 resulted in higher intracellular xylitol concentrations but did not significantly change the intracellular NAD ؉ / NADH ratio in xylose-fermenting strains. The results demonstrate that Fps1p is involved in xylitol export in S. cerevisiae and present a new gene deletion target, FPS1, and a mechanism different from those previously reported to engineer yeast for improved xylose fermentation.

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Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis

Cited by 451 publications

References 48 publications

Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom

Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom

Polymorphisms in Multiple Genes Contribute to the Spontaneous Mitochondrial Genome Instability ofSaccharomyces cerevisiaeS288C Strains

Deletion of FPS1 , Encoding Aquaglyceroporin Fps1p, Improves Xylose Fermentation by Engineered Saccharomyces cerevisiae

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