The use of plant biomass for biofuel production will require efficient utilization of the sugars in lignocellulose, primarily glucose and xylose. However, strains of Saccharomyces cerevisiae presently used in bioethanol production ferment glucose but not xylose. Yeasts engineered to ferment xylose do so slowly, and cannot utilize xylose until glucose is completely consumed. To overcome these bottlenecks, we engineered yeasts to coferment mixtures of xylose and cellobiose. In these yeast strains, hydrolysis of cellobiose takes place inside yeast cells through the action of an intracellular β-glucosidase following import by a high-affinity cellodextrin transporter. Intracellular hydrolysis of cellobiose minimizes glucose repression of xylose fermentation allowing coconsumption of cellobiose and xylose. The resulting yeast strains, cofermented cellobiose and xylose simultaneously and exhibited improved ethanol yield when compared to fermentation with either cellobiose or xylose as sole carbon sources. We also observed improved yields and productivities from cofermentation experiments performed with simulated cellulosic hydrolyzates, suggesting this is a promising cofermentation strategy for cellulosic biofuel production. The successful integration of cellobiose and xylose fermentation pathways in yeast is a critical step towards enabling economic biofuel production.

Improving Yeast for Biofuel Production: The biofuels industry uses the yeast Saccharomyces cerevisiae to produce ethanol from sugars derived from cornstarch or sugar cane. Plant cell walls are an attractive sugar source; however, yeast does not grow efficiently on cellulose–derived sugars (cellodextrins). Galazka et al. (p. 84 , published online 9 September) now show that a model cellolytic fungus Neurospora crassa relies on a cellodextrin transport system to facilitate growth on cellulose. Yeast reconstituted with this transport system grew efficiently on cellodextrins, which could potentially improve the efficiency of cellulosic biofuel production.

Eukaryotic genomes are organized into chromatin domains with three-dimensional arrangements that presumably result from interactions between the chromatin constituents—proteins, DNA, and RNA—within the physical constraints of the nucleus. We used chromosome conformation capture (3C) followed by high-throughput sequencing (Hi-C) with wild-type and mutant strains of Neurospora crassa to gain insight into the role of heterochromatin in the organization and function of the genome. We tested the role of three proteins thought to be important for establishment of heterochromatin, namely, the histone H3 lysine 9 methyltransferase DIM-5, Heterochromatin Protein 1 (HP1), which specifically binds to the product of DIM-5 (trimethylated H3 lysine 9 [H3K9me3]), and DIM-3 (importin alpha), which is involved in DIM-5 localization. The average genome configuration of the wild-type strain revealed strong intra- and inter-chromosomal associations between both constitutive and facultative heterochromatic domains, with the strongest interactions among the centromeres, subtelomeres, and interspersed heterochromatin. Surprisingly, loss of either H3K9me3 or HP1 had only mild effects on heterochromatin compaction, whereas dim-3 caused more drastic changes, specifically decreasing interactions between constitutive heterochromatic domains. Thus, associations between heterochromatic regions are a major component of the chromosome conformation in Neurospora, but two widely studied key heterochromatin proteins are not necessary, implying that undefined protein factors play key roles in maintaining overall chromosome organization.

Significance: Two forms of heterochromatin, constitutive and facultative, cause gene silencing in eukaryotes. In Neurospora crassa , H3K27me2/3-marked facultative heterochromatin reversibly represses scores of specialized genes, whereas H3K9me3-marked constitutive heterochromatin permanently silences repetitive DNA. Interactions between heterochromatin provide a structural framework for the genome, and this is thought to be functionally important. Histone marks underlying constitutive and facultative heterochromatin are nonessential in N. crassa , permitting tests of their roles in genome organization and gene expression. Although linkages between regions of constitutive heterochromatin are the most prominent feature of the 3D structure of the genome, loss of the facultative mark has a much greater effect on genome architecture than does loss of key features of constitutive heterochromatin, i.e., H3K9me3 and Heterochromatin Protein 1.