Comparative genomics of xylose-fermenting fungi for enhanced biofuel production

Wohlbach, Dana J.; Kuo, Alan; Sato, Trey K.; Potts, Katlyn M.; Salamov, Asaf; LaButti, Kurt; Sun, Hui; Clum, Alicia; Pangilinan, Jasmyn; Lindquist, Erika; Lucas, Susan; Lapidus, Alla; Jin, Mingjie; Gunawan, Christa; Balan, Venkatesh; Dale, Bruce E.; Jeffries, Thomas W.; Zinkel, Robert A.; Barry, Kerrie; Grigoriev, Igor V.; Gasch, Audrey P.

doi:10.1073/pnas.1103039108

Cited by 172 publications

(176 citation statements)

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“…In the present work, we report that an unusual native xylosefermenting yeast, Spathaspora passalidarum NN245 (15,30,46), coassimilates xylose and glucose aerobically, uses xylose faster than glucose when the sugars are presented individually, and coferments glucose, xylose, and cellobiose from mixtures of pure sugars or hydrolysates under oxygen-limiting conditions. These features make S. passalidarum potentially useful for simultaneous saccharification and fermentation (SSF) and for studying enzymatic and regulatory mechanisms enabling simultaneous utilization of cellulosic and hemicellulosic sugars.…”

mentioning

confidence: 77%

Cofermentation of Glucose, Xylose, and Cellobiose by the Beetle-Associated Yeast Spathaspora passalidarum

Headman

et al. 2012

Appl Environ Microbiol

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125

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dFermentation of cellulosic and hemicellulosic sugars from biomass could resolve food-versus-fuel conflicts inherent in the bioconversion of grains. However, the inability to coferment glucose and xylose is a major challenge to the economical use of lignocellulose as a feedstock. Simultaneous cofermentation of glucose, xylose, and cellobiose is problematic for most microbes because glucose represses utilization of the other saccharides. Surprisingly, the ascomycetous, beetle-associated yeast Spathaspora passalidarum, which ferments xylose and cellobiose natively, can also coferment these two sugars in the presence of 30 g/liter glucose. S. passalidarum simultaneously assimilates glucose and xylose aerobically, it simultaneously coferments glucose, cellobiose, and xylose with an ethanol yield of 0.42 g/g, and it has a specific ethanol production rate on xylose more than 3 times that of the corresponding rate on glucose. Moreover, an adapted strain of S. passalidarum produced 39 g/liter ethanol with a yield of 0.37 g/g sugars from a hardwood hydrolysate. Metabolome analysis of S. passalidarum before onset and during the fermentations of glucose and xylose showed that the flux of glycolytic intermediates is significantly higher on xylose than on glucose. The high affinity of its xylose reductase activities for NADH and xylose combined with allosteric activation of glycolysis probably accounts in part for its unusual capacities. These features make S. passalidarum very attractive for studying regulatory mechanisms enabling bioconversion of lignocellulosic materials by yeasts.

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mentioning

confidence: 77%

Cofermentation of Glucose, Xylose, and Cellobiose by the Beetle-Associated Yeast Spathaspora passalidarum

Headman

et al. 2012

Appl Environ Microbiol

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125

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“…ML support was estimated with 1000 bootstrap replicates. Alignments and trees were deposited in TreeBASE (accession number S13305).The sequences for RPB1 and XR were obtained with SEQUIN 11.9 (http:// www.ncbi.nlm.nih.gov/Sequin/) with an alternative yeast nuclear codon bias (Ohama et al 1993, Wohlbach et al 2011. Tree editing was done with FigTree 1.3.1 software (http://tree.bio.ed.ac.uk/software/figtree/).…”

Section: Methodsmentioning

confidence: 99%

Scheffersomyces cryptocercus: a new xylose-fermenting yeast associated with the gut of wood roaches and new combinations in theSugiyamaellayeast clade

2013

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The gut of wood-feeding insects is a microhabitat for a specialized community of microbes, including bacteria and several groups of eukaryotes such as nematodes, parabasalids and fungi. The characterization of gut yeast communities from a variety of insects has shown that certain yeasts often are associated with the insects. The gut of woodfeeding insects is rich in ascomycete yeasts and in particular xylose-fermenting (X-F) and assimilating yeasts have been consistently present in the gut of lignicolous insects. The objective of this study was the characterization of the yeast flora from the gut of the wood roach Cryptocercus sp. (Blattodea: Cryptocercidae). Five wood roaches were collected along the Appalachian Trail near the border between Tennessee and North Carolina, USA. We isolated 18 yeast strains from the wood roaches identified as Sugiyamaella paludigena and Sugiyamaella lignohabitans, xylose-assimilating yeasts, and Scheffersomyces cryptocercus (NRRL Y-48824 T 5 CBS 12658) a new species of X-F yeast. The presence of X-F and certain non X-F yeasts in the gut of the subsocial wood roach Cryptocercus sp. extends the previous findings of associations between certain ascomycete yeasts and lignicolous insects. New combinations were made for 13 asexual members of the Sugiyamaella clade.

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“…Arrays were scanned and analyzed with a GenePix4000 scanner (Molecular Devices, Sunnyvale, CA), and the background-subtracted signal from both channels was extracted with the program NimbleScan. Data normalization was performed using quantile normalization of the pooled array data as in Wohlbach et al (2011). Expression differences in response to ethanol were taken as the log 2 ratio of the red/green signal from the arrays.…”

Section: Microarray Hybridization and Analysismentioning

confidence: 99%

Genetic Architecture of Ethanol-Responsive Transcriptome Variation in Saccharomyces cerevisiae Strains

et al. 2014

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Natural variation in gene expression is pervasive within and between species, and it likely explains a significant fraction of phenotypic variation between individuals. Phenotypic variation in acute systemic responses can also be leveraged to reveal physiological differences in how individuals perceive and respond to environmental perturbations. We previously found extensive variation in the transcriptomic response to acute ethanol exposure in two wild isolates and a common laboratory strain of Saccharomyces cerevisiae. Many expression differences persisted across several modules of coregulated genes, implicating trans-acting systemic differences in ethanol sensing and/or response. Here, we conducted expression QTL mapping of the ethanol response in two strain crosses to identify the genetic basis for these differences. To understand systemic differences, we focused on "hotspot" loci that affect many transcripts in trans. Candidate causal regulators contained within hotspots implicate upstream regulators as well as downstream effectors of the ethanol response. Overlap in hotspot targets revealed additive genetic effects of trans-acting loci as well as "epihotspots," in which epistatic interactions between two loci affected the same suites of downstream targets. One epi-hotspot implicated interactions between Mkt1p and proteins linked to translational regulation, prompting us to show that Mkt1p localizes to P bodies upon ethanol stress in a strain-specific manner. Our results provide a glimpse into the genetic architecture underlying natural variation in a stress response and present new details on how yeast respond to ethanol stress. N ATURAL variation in gene expression is hypothesized to be a major source of phenotypic variation between individuals (King and Wilson 1975;Oleksiak et al. 2002). Gene expression variation underlies differences in susceptibility to infectious disease (Li et al. 2010;Barreiro et al. 2012), drug sensitivity (Fay et al. 2004;Kvitek et al. 2008;Maranville et al. 2011;Hodgins-Davis et al. 2012;Chang et al. 2013), inflammation (Gargalovic et al. 2006Orozco et al. 2012), cardiovascular disease (Romanoski et al. 2010), metabolism (Fraser et al. 2010Rossouw et al. 2012;Skelly et al. 2013), morphology (Yvert et al. 2003Chin et al. 2012;Skelly et al. 2013), and even behavior (Ziebarth et al. 2012). Still, identifying the genetic and molecular mechanisms that underlie the expression variation is a major challenge.Expression quantitative trait loci (eQTL) mapping (reviewed in Gilad et al. 2008) is a powerful approach to dissect the genetic basis of expression differences. Transcript abundance is treated as a quantitative trait whose genetic determinants can be implicated by well-established linkage mapping techniques. The first eQTL studies in yeast illuminated the genetic landscape of gene expression-variation determinants under standard growth conditions (Brem et al. 2002;Yvert et al. 2003). Subsequent eQTL studies surveyed the genetic control of transcript abundance in Arabidopsi...

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Comparative genomics of xylose-fermenting fungi for enhanced biofuel production

Cited by 172 publications

References 51 publications

Cofermentation of Glucose, Xylose, and Cellobiose by the Beetle-Associated Yeast Spathaspora passalidarum

Cofermentation of Glucose, Xylose, and Cellobiose by the Beetle-Associated Yeast Spathaspora passalidarum

Scheffersomyces cryptocercus: a new xylose-fermenting yeast associated with the gut of wood roaches and new combinations in theSugiyamaellayeast clade

Genetic Architecture of Ethanol-Responsive Transcriptome Variation in Saccharomyces cerevisiae Strains

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