Draft Genome Sequence of Saccharomyces cerevisiae IR-2, a Useful Industrial Strain for Highly Efficient Production of Bioethanol

Molecular evolutionary engineering of xylose isomerase to improve its catalytic activity and performance of micro-aerobic glucose/xylose co-fermentation in Saccharomyces cerevisiae

BACKGROUND

Expression of d-xylose isomerase having high catalytic activity in Saccharomyces cerevisiae (S. cerevisiae) is a prerequisite for efficient and economical production of bioethanol from cellulosic biomass. Although previous studies demonstrated functional expression of several xylose isomerases (XI) in S. cerevisiae, identification of XIs having higher catalytic activity is needed. Here, we report a new strategy to improve xylose fermentation in the S. cerevisiae strain IR-2 that involves an evolutionary engineering to select top-performing XIs from eight previously reported XIs derived from various species.

RESULTS

Eight XI genes shown to have good expression in S. cerevisiae were introduced into the strain IR-2 having a deletion of GRE3 and XKS1 overexpression that allows use of d-xylose as a carbon source. Each transformant was evaluated under aerobic and micro-aerobic culture conditions. The strain expressing XI from Lachnoclostridium phytofermentans ISDg (LpXI) had the highest d-xylose consumption rate after 72 h of micro-aerobic fermentation on d-glucose and d-xylose mixed medium. To enhance LpXI catalytic activity, we performed random mutagenesis using error-prone polymerase chain reaction (PCR), which yielded two LpXI candidates, SS82 and SS92, that showed markedly improved fermentation performance. The LpXI genes in these clones carried either T63I or V162A/N303T point mutations. The SS120 strain expressing LpXI with the double mutation of T63I/V162A assimilated nearly 85 g/L d-glucose and 35 g/L d-xylose to produce 53.3 g/L ethanol in 72 h with an ethanol yield of approximately 0.44 (g/g-input sugars). An in vitro enzyme assay showed that, compared to wild-type, the LpXI double mutant in SS120 had a considerably higher V _max (0.107 µmol/mg protein/min) and lower K _m (37.1 mM).

CONCLUSIONS

This study demonstrated that LpXI has the highest d-xylose consumption rate among the XIs expressed in IR-2 under micro-aerobic co-fermentation conditions. A combination of novel mutations (T63I and V162A) significantly improved the enzymatic activity of LpXI, indicating that LpXI-T63I/V162A would be a potential construct for highly efficient production of cellulosic ethanol.

Whole-Genome Sequence of an Isogenic Haploid Strain, Saccharomyces cerevisiae IR-2idA30(MATa), Established from the Industrial Diploid Strain IR-2

We present the draft genome sequence of an isogenic haploid strain, IR-2idA30(MATa), established from Saccharomyces cerevisiae IR-2. Assembly of long reads and previously obtained contigs from the genome of diploid IR-2 resulted in 50 contigs, and the variations and sequencing errors were corrected by short reads.

We present the draft genome sequence of an isogenic haploid strain, IR-2idA30(MATa), established from Saccharomyces cerevisiae IR-2. Assembly of long reads and previously obtained contigs from the genome of diploid IR-2 resulted in 50 contigs, and the variations and sequencing errors were corrected by short reads.

Systematic optimization of gene expression of pentose phosphate pathway enhances ethanol production from a glucose/xylose mixed medium in a recombinant Saccharomyces cerevisiae

The pentose phosphate pathway (PPP) plays an important role in the synthesis of ribonucleotides and aromatic amino acids. During bioethanol production from cellulosic biomass composed mainly of d-glucose and d-xylose, the PPP is also involved in xylose metabolism by engineered Saccharomyces cerevisiae. Although the activities and thermostabilities of the four PPP enzymes (transaldolase: TAL1, transketolase: TKL1, ribose-5-phosphate ketol-isomerase: RKI1 and d-ribulose-5-phosphate 3-epimerase: RPE1) can affect the efficiency of cellulosic ethanol production at high temperatures, little is known about the suitable expression levels of these PPP genes. Here, we overexpressed PPP genes from S. cerevisiae and the thermotolerant yeast Kluyveromyces marxianus either singly or in combination in recombinant yeast strains harboring a mutant of xylose isomerase (XI) and evaluated xylose consumption and ethanol production of these yeast transformants in glucose/xylose mixed media at 36 °C. Among the PPP genes examined, we found that: (1) strains that overexpressed S. cerevisiae TKL1 exhibited the highest rate of xylose consumption relative to strains that overexpressed other PPP genes alone; (2) overexpression of RKI1 and TAL1 derived from K. marxianus with S. cerevisiae TKL1 increased the xylose consumption rate by 1.87-fold at 24 h relative to the control strain (from 0.55 to 1.03 g/L/h); (3) the strains with XI showed higher ethanol yield than strains with xylose reductase and xylitol dehydrogenase and (4) PHO13 disruption did not improve xylose assimilation under the experimental conditions. Together these results indicated that optimization of PPP activity improves xylose metabolism in genetically engineered yeast strains, which could be useful for commercial production of ethanol from cellulosic material.

Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research

The genome sequences of more than 100 strains of the yeast Saccharomyces cerevisiae have been published. Unfortunately, most of these genome assemblies contain dozens to hundreds of gaps at repetitive sequences, including transposable elements, tRNAs, and subtelomeric regions, which is where novel genes generally reside. Relatively few strains have been chosen for genome sequencing based on their biofuel production potential, leaving an additional knowledge gap. Here, we describe the nearly complete genome sequence of GLBRCY22-3 (Y22-3), a strain of S. cerevisiae derived from the stress-tolerant wild strain NRRL YB-210 and subsequently engineered for xylose metabolism. After benchmarking several genome assembly approaches, we developed a pipeline to integrate Pacific Biosciences (PacBio) and Illumina sequencing data and achieved one of the highest quality genome assemblies for any S. cerevisiae strain. Specifically, the contig N50 is 693 kbp, and the sequences of most chromosomes, the mitochondrial genome, and the 2-micron plasmid are complete. Our annotation predicts 92 genes that are not present in the reference genome of the laboratory strain S288c, over 70% of which were expressed. We predicted functions for 43 of these genes, 28 of which were previously uncharacterized and unnamed. Remarkably, many of these genes are predicted to be involved in stress tolerance and carbon metabolism and are shared with a Brazilian bioethanol production strain, even though the strains differ dramatically at most genetic loci. The Y22-3 genome sequence provides an exceptionally high-quality resource for basic and applied research in bioenergy and genetics.