Biology subjects

Serate, J.

Publications and source records attributed to Serate, J..

4 recordsLinked to original sources

bioRxiv2025

An evolved strain of Spathaspora passalidarum produces ethanol from sugarcane bagasse and switchgrass lignocellulosic hydrolysates

Lignocellulosic hydrolysates, derived from plant biomass, contain various inhibitors that can hinder microbial growth. This study aimed to enable the growth and ethanol production by the xylose-fermenting yeast Spathaspora passalidarum in the presence of lignocellulosic hydrolysate inhibitors, particularly acetic acid. Ultraviolet (UV)-induced mutagenesis and adaptive laboratory evolution (ALE) were used to select for mutants with higher tolerance to these inhibitors. The initial mutant strain, MT01, was selected for increased growth in medium containing xylose and acetic acid. This strain underwent further evolution, resulting in the strain ME3.5.5, which showed significant improvements in both growth and ethanol production compared to the parental strain when tested in sugarcane bagasse hemicellulosic hydrolysate (SBHH). Genomic analysis identified non-synonymous and frameshift mutations in four genes, including CYR1 (encoding adenylate cyclase). These findings suggest that genetically optimized S. passalidarum strains could play a crucial role in advancing industrial bioethanol production from lignocellulosic biomass by overcoming the inhibitory effects of compounds found in lignocellulosic hydrolysates.

genomics↗

bioRxiv2025

pH adjustment increases biofuel production from inhibitory switchgrass hydrolysates

Biofuels derived from renewable and sustainable lignocellulosic biomass, such as switchgrass, offer a promising means to limit greenhouse gas emissions. However, switchgrass grown under drought conditions contains high levels of chemical compounds that inhibit microbial conversion to biofuels. Fermentation of drought switchgrass hydrolysates by engineered Saccharomyces cerevisiae and Zymomonas mobilis generates less ethanol than fermentation of hydrolyzed switchgrass from an average rainfall year. Here, we demonstrate that this inhibitory effect can be alleviated by altering the pH of drought-switchgrass hydrolysates made from two different pretreatment methods: Ammonia Fiber Expansion (AFEX) and Soaking in Aqueous Ammonia (SAA). Fermentation rates and biofuel production from AFEX- and SAA-pretreated switchgrass hydrolysates from normal and drought years were higher at pH 5.8 than at pH 5.0 for both Saccharomyces cerevisiae and Zymomonas mobilis. Additionally, SAA pretreatment of drought switchgrass enabled increased fermentation rates and titers compared to AFEX pretreatment. Using a synthetic mimic of switchgrass hydrolysate, we identified relief from pH-dependent inhibition by lignocellulose-derived inhibitors as the cause of increased biofuel production above a pH of 5.0. These results demonstrate that SAA pretreatment and pH adjustment can significantly improve fermentation and biofuel production from switchgrass hydrolysates and especially from drought-switchgrass hydrolysates by industrial microorganisms.

microbiology↗

bioRxiv2017

Chemical genomic guided engineering of gamma-valerolactone tolerant yeast

BackgroundGamma valerolactone (GVL) is a promising technology for degradation of biomass for biofuel production; however, GVL has adverse toxicity effects on fermentative microbes. Using a combination of chemical genomics and chemical proteomics we sought to understand the mechanism toxicity and resistance to GVL with the goal of engineering a GVL-tolerant, xylose-fermenting yeast.\n\nResultsChemical genomic profiling of GVL predicted that this chemical affects membranes and membrane-bound processes. We show that GVL causes rapid, dose-dependent cell permeability, and is synergistic with ethanol. Chemical genomic profiling of GVL revealed that deletion of the functionally related enzymes Pad1p and Fdc1p, which act together to decarboxylate phenolic acids to vinyl derivatives, increases yeast tolerance to GVL. Further, overexpression of Pad1p sensitizes cells to GVL toxicity. To improve GVL tolerance, we deleted PAD1 and FDC1 in a xylose-fermenting yeast strain. The modified strain exhibited increased anaerobic growth, sugar utilization, and ethanol production in synthetic hydrolysate with 1.5% GVL, and under other conditions. Chemical proteomic profiling of the engineered strain revealed that enzymes involved in ergosterol biosynthesis were more abundant in the presence of GVL compared to the background strain. The engineered GVL strain contained greater amounts of ergosterol than the background strain.\n\nConclusionsWe found that GVL exerts toxicity to yeast by compromising cellular membranes, and that this toxicity is synergistic with ethanol. Deletion of PAD1 and FDC1 conferred GVL resistance to a xylose-fermenting yeast strain by increasing ergosterol content in cells. The GVL-tolerant strain fermented sugars in the presence of GVL levels that were inhibitory to the unmodified strain. This strain represents a xylose fermenting yeast specifically tailored to GVL produced hydrolysates

bioengineering↗

bioRxiv2016

Inhibition of microbial biofuel production in drought stressed switchgrass hydrolysate

BackgroundInterannual variability in precipitation, particularly drought, can affect lignocellulosic crop biomass yields and composition, and is expected to increase biofuel yield variability. However, the effect of precipitation on downstream fermentation processes has never been directly characterized. In order to investigate the impact of interannual climate variability on biofuel production, corn stover and switchgrass were collected during three years with significantly different precipitation profiles, representing a major drought year (2012) and two years with average precipitation for the entire season (2010 and 2013). All feedstocks were AFEX (ammonia fiber expansion)-pretreated, enzymatically hydrolyzed, and the hydrolysates separately fermented using xylose-utilizing strains of Saccharomyces cerevisiae and Zymomonas mobilis. A chemical genomics approach was also used to evaluate the growth of yeast mutants in the hydrolysates.\n\nResultsWhile most corn stover and switchgrass hydrolysates were readily fermented, growth of S. cerevisiae was completely inhibited in hydrolysate generated from drought stressed switchgrass. Based on chemical genomics analysis, yeast strains deficient in genes related to protein trafficking within the cell were significantly more resistant to the drought year switchgrass hydrolysate. Detailed biomass and hydrolysate characterization revealed that switchgrass accumulated greater concentrations of soluble sugars in response to the drought and these sugars were subsequently degraded to pyrazines and imidazoles during ammonia-based pretreatment. When added ex situ to normal switchgrass hydrolysate, imidazoles and pyrazines caused anaerobic growth inhibition of S. cerevisiae.\n\nConclusionsIn response to the osmotic pressures experienced during drought stress, plants accumulate soluble sugars that are susceptible to degradation during chemical pretreatments. For ammonia-based pretreatment these sugars degrade to imidazoles and pyrazines. These compounds contribute to S. cerevisiae growth inhibition in drought year switchgrass hydrolysate. This work discovered that variation in environmental conditions during the growth of bioenergy crops could have significant detrimental effects on fermentation organisms during biofuel production. These findings are relevant to regions where climate change is predicted to cause an increased incidence of drought and to marginal lands with poor water holding capacity, where fluctuations in soil moisture may trigger frequent drought stress response in lignocellulosic feedstocks.

microbiology↗