scholarly journals Transcriptomic Changes Induced by Deletion of Transcriptional Regulator GCR2 on Pentose Sugar Metabolism in Saccharomyces cerevisiae

2021 ◽  
Vol 9 ◽  
Author(s):  
Minhye Shin ◽  
Heeyoung Park ◽  
Sooah Kim ◽  
Eun Joong Oh ◽  
Deokyeol Jeong ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Xylose Fermentation ◽  
Sugar Metabolism ◽  
Pentose Phosphate ◽  
Biofuel Production ◽  
Rna Seq ◽  
Loss Of Function ◽  
Lignocellulosic Biofuel ◽  
Pentose Sugar ◽  
Transcriptomic Changes

Being a microbial host for lignocellulosic biofuel production, Saccharomyces cerevisiae needs to be engineered to express a heterologous xylose pathway; however, it has been challenging to optimize the engineered strain for efficient and rapid fermentation of xylose. Deletion of PHO13 (Δpho13) has been reported to be a crucial genetic perturbation in improving xylose fermentation. A confirmed mechanism of the Δpho13 effect on xylose fermentation is that the Δpho13 transcriptionally activates the genes in the non-oxidative pentose phosphate pathway (PPP). In the current study, we found a couple of engineered strains, of which phenotypes were not affected by Δpho13 (Δpho13-negative), among many others we examined. Genome resequencing of the Δpho13-negative strains revealed that a loss-of-function mutation in GCR2 was responsible for the phenotype. Gcr2 is a global transcriptional factor involved in glucose metabolism. The results of RNA-seq confirmed that the deletion of GCR2 (Δgcr2) led to the upregulation of PPP genes as well as downregulation of glycolytic genes, and changes were more significant under xylose conditions than those under glucose conditions. Although there was no synergistic effect between Δpho13 and Δgcr2 in improving xylose fermentation, these results suggested that GCR2 is a novel knockout target in improving lignocellulosic ethanol production.

scholarly journals Transcriptomic changes induced by de-activation of lower glycolysis and its advantage on pentose sugar metabolism in Saccharomyces cerevisiae

2021 ◽  
Author(s):  
Minhye Shin ◽  
Heeyoung Park ◽  
Sooah Kim ◽  
Eun Joong Oh Oh ◽  
Deokyeol Jeong ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Metabolic Regulation ◽  
Xylose Fermentation ◽  
Sugar Metabolism ◽  
Pentose Phosphate ◽  
Biofuel Production ◽  
Loss Of Function ◽  
Cellulosic Biofuel ◽  
Pentose Sugar ◽  
Positive Effect

As a microbial host for cellulosic biofuel production, Saccharomyces cerevisiae needs to be engineered to express a heterologous xylose pathway. However, it has been challenging to optimize the engineered strain for efficient and rapid fermentation of xylose. Deletion of PHO13 (pho13) has been reported to be a crucial genetic perturbation for improving xylose fermentation. A confirmed mechanism of the pho13-positive effect on xylose fermentation is that the deletion of PHO13 transcriptionally activates the genes in the non-oxidative pentose phosphate pathway (PPP). In the present study, we reported that a pho13-positive effect was not observed from a couple of engineered strains, among the many others we have examined. To extend our knowledge of pho13-mediated metabolic regulation, we performed genome sequencing of pho13-negative strains. We identified a loss-of-function mutation in GCR2 responsible for the pho13-negative phenotype. Gcr2 is a transcriptional activator of the lower glycolytic pathway. Thus, the deletion of GCR2 (gcr2) led to deactivation of lower glycolysis as confirmed by RNA-seq. Also, gcr2 resulted in the up-regulation of PPP genes, which explains the improved xylose fermentation of gcr2 mutants. As pho13 and gcr2 cause similar transcriptional changes with PPP genes, there was no synergistic effect between pho13 and gcr2 for improving xylose fermentation. The present study identified GCR2 as a new knockout target to improve xylose fermentation and cellulosic biofuel production. Now published in Frontiers in Bioengineering and Biotechnology doi: 10.3389/fbioe.2021.654177

scholarly journals Hierarchy in Pentose Sugar Metabolism in Clostridium acetobutylicum

2014 ◽  
Vol 81 (4) ◽  
pp. 1452-1462 ◽  
Author(s):  
Ludmilla Aristilde ◽  
Ian A. Lewis ◽  
Junyoung O. Park ◽  
Joshua D. Rabinowitz
Keyword(s):  
Clostridium Acetobutylicum ◽  
Sugar Metabolism ◽  
Pentose Phosphate ◽  
Acetyl Phosphate ◽  
Content Type ◽  
Acetate Excretion ◽  
Terrestrial Carbon Cycle ◽  
Pentose Sugar ◽  
Phosphoketolase Pathway ◽  
Pentose Sugars

ABSTRACTBacterial metabolism of polysaccharides from plant detritus into acids and solvents is an essential component of the terrestrial carbon cycle. Understanding the underlying metabolic pathways can also contribute to improved production of biofuels. Using a metabolomics approach involving liquid chromatography-mass spectrometry, we investigated the metabolism of mixtures of the cellulosic hexose sugar (glucose) and hemicellulosic pentose sugars (xylose and arabinose) in the anaerobic soil bacteriumClostridium acetobutylicum. Simultaneous feeding of stable isotope-labeled glucose and unlabeled xylose or arabinose revealed that, as expected, glucose was preferentially used as the carbon source. Assimilated pentose sugars accumulated in pentose phosphate pathway (PPP) intermediates with minimal flux into glycolysis. Simultaneous feeding of xylose and arabinose revealed an unexpected hierarchy among the pentose sugars, with arabinose utilized preferentially over xylose. The phosphoketolase pathway (PKP) provides an alternative route of pentose catabolism inC. acetobutylicumthat directly converts xylulose-5-phosphate into acetyl-phosphate and glyceraldehyde-3-phosphate, bypassing most of the PPP. When feeding the mixture of pentose sugars, the labeling patterns of lower glycolytic intermediates indicated more flux through the PKP than through the PPP and upper glycolysis, and this was confirmed by quantitative flux modeling. Consistent with direct acetyl-phosphate production from the PKP, growth on the pentose mixture resulted in enhanced acetate excretion. Taken collectively, these findings reveal two hierarchies in clostridial pentose metabolism: xylose is subordinate to arabinose, and the PPP is used less than the PKP.

scholarly journals Engineering Redox Cofactor Regeneration for Improved Pentose Fermentation in Saccharomyces cerevisiae

2003 ◽  
Vol 69 (10) ◽  
pp. 5892-5897 ◽  
Author(s):  
Ritva Verho ◽  
John Londesborough ◽  
Merja Penttilä ◽  
Peter Richard
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genetic Engineering ◽  
Pentose Phosphate Pathway ◽  
Yeast Strain ◽  
Redox Reactions ◽  
Xylose Fermentation ◽  
Pentose Phosphate ◽  
Anaerobic Conditions ◽  
Nadph Regeneration ◽  
Glucose 6 Phosphate Dehydrogenase

ABSTRACT Pentose fermentation to ethanol with recombinant Saccharomyces cerevisiae is slow and has a low yield. A likely reason for this is that the catabolism of the pentoses d-xylose and l-arabinose through the corresponding fungal pathways creates an imbalance of redox cofactors. The process, although redox neutral, requires NADPH and NAD+, which have to be regenerated in separate processes. NADPH is normally generated through the oxidative part of the pentose phosphate pathway by the action of glucose-6-phosphate dehydrogenase (ZWF1). To facilitate NADPH regeneration, we expressed the recently discovered gene GDP1, which codes for a fungal NADP+-dependent d-glyceraldehyde-3-phosphate dehydrogenase (NADP-GAPDH) (EC 1.2.1.13), in an S. cerevisiae strain with the d-xylose pathway. NADPH regeneration through an NADP-GAPDH is not linked to CO2 production. The resulting strain fermented d-xylose to ethanol with a higher rate and yield than the corresponding strain without GDP1; i.e., the levels of the unwanted side products xylitol and CO2 were lowered. The oxidative part of the pentose phosphate pathway is the main natural path for NADPH regeneration. However, use of this pathway causes wasteful CO2 production and creates a redox imbalance on the path of anaerobic pentose fermentation to ethanol because it does not regenerate NAD+. The deletion of the gene ZWF1 (which codes for glucose-6-phosphate dehydrogenase), in combination with overexpression of GDP1 further stimulated d-xylose fermentation with respect to rate and yield. Through genetic engineering of the redox reactions, the yeast strain was converted from a strain that produced mainly xylitol and CO2 from d-xylose to a strain that produced mainly ethanol under anaerobic conditions.

scholarly journals Harnessing Genetic Diversity in Saccharomyces cerevisiae for Fermentation of Xylose in Hydrolysates of Alkaline Hydrogen Peroxide-Pretreated Biomass

2013 ◽  
Vol 80 (2) ◽  
pp. 540-554 ◽  
Author(s):  
Trey K. Sato ◽  
Tongjun Liu ◽  
Lucas S. Parreiras ◽  
Daniel L. Williams ◽  
Dana J. Wohlbach ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Hydrogen Peroxide ◽  
Rapid Evolution ◽  
Biofuel Production ◽  
Ecological Niches ◽  
Alkaline Hydrogen Peroxide ◽  
Xylose Metabolism ◽  
Content Type ◽  
Inhibitory Compounds ◽  
Lignocellulosic Biofuel

ABSTRACTThe fermentation of lignocellulose-derived sugars, particularly xylose, into ethanol by the yeastSaccharomyces cerevisiaeis known to be inhibited by compounds produced during feedstock pretreatment. We devised a strategy that combined chemical profiling of pretreated feedstocks, high-throughput phenotyping of genetically diverseS. cerevisiaestrains isolated from a range of ecological niches, and directed engineering and evolution against identified inhibitors to produce strains with improved fermentation properties. We identified and quantified for the first time the major inhibitory compounds in alkaline hydrogen peroxide (AHP)-pretreated lignocellulosic hydrolysates, including Na+, acetate, andp-coumaric (pCA) and ferulic (FA) acids. By phenotyping these yeast strains for their abilities to grow in the presence of these AHP inhibitors, one heterozygous diploid strain tolerant to all four inhibitors was selected, engineered for xylose metabolism, and then allowed to evolve on xylose with increasing amounts ofpCA and FA. After only 149 generations, one evolved isolate, GLBRCY87, exhibited faster xylose uptake rates in both laboratory media and AHP switchgrass hydrolysate than its ancestral GLBRCY73 strain and completely converted 115 g/liter of total sugars in undetoxified AHP hydrolysate into more than 40 g/liter ethanol. Strikingly, genome sequencing revealed that during the evolution from GLBRCY73, the GLBRCY87 strain acquired the conversion of heterozygous to homozygous alleles in chromosome VII and amplification of chromosome XIV. Our approach highlights that simultaneous selection on xylose andpCA or FA with a wildS. cerevisiaestrain containing inherent tolerance to AHP pretreatment inhibitors has potential for rapid evolution of robust properties in lignocellulosic biofuel production.

scholarly journals PKA and HOG signaling contribute separable roles to anaerobic xylose fermentation in yeast engineered for biofuel production

2019 ◽  
Author(s):  
Ellen R. Wagner ◽  
Kevin S. Myers ◽  
Nicholas M. Riley ◽  
Joshua J. Coon ◽  
Audrey P. Gasch
Keyword(s):  
Stress Tolerance ◽  
Corn Stover ◽  
Xylose Fermentation ◽  
Glucose Consumption ◽  
Negative Regulator ◽  
Biofuel Production ◽  
Regulatory Subunit ◽  
Loss Of Function ◽  
Activity Increase ◽  
Xylose Consumption

AbstractLignocellulosic biomass offers a sustainable source for biofuel production that does not compete with food-based cropping systems. Importantly, two critical bottlenecks prevent economic adoption: many industrially relevant microorganisms cannot ferment pentose sugars prevalent in lignocellulosic medium, leaving a significant amount of carbon unutilized. Furthermore, chemical biomass pretreatment required to release fermentable sugars generates a variety of toxins, which inhibit microbial growth and metabolism, specifically limiting pentose utilization in engineered strains. Here we dissected genetic determinants of anaerobic xylose fermentation and stress tolerance in chemically pretreated corn stover biomass, called hydrolysate. We previously revealed that loss-of-function mutations in the stress-responsive MAP kinaseHOG1and negative regulator of the RAS/Protein Kinase A (PKA) pathway,IRA2, enhances anaerobic xylose fermentation. However, these mutations likely reduce cells’ ability to tolerate the toxins present in lignocellulosic hydrolysate, making the strain especially vulnerable to it. We tested the contributions of Hog1 and PKA signaling via IRA2 or PKA negative regulatory subunit BCY1 to metabolism, growth, and stress tolerance in corn stover hydrolysate and laboratory medium with mixed sugars. We found mutations causing upregulated PKA activity increase growth rate and glucose consumption in various media but do not have a specific impact on xylose fermentation. In contrast, mutation ofHOG1specifically increased xylose usage. We hypothesized improving stress tolerance would enhance the rate of xylose consumption in hydrolysate. Surprisingly, increasing stress tolerance did not augment xylose fermentation in lignocellulosic medium in this strain background, suggesting other mechanisms besides cellular stress limit this strain’s ability for anaerobic xylose fermentation in hydrolysate.

scholarly journals Transcriptome Profile Alterations with Carbon Nanotubes, Quantum Dots, and Silver Nanoparticles: A Review

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 794
Author(s):  
Cullen Horstmann ◽  
Victoria Davenport ◽  
Min Zhang ◽  
Alyse Peters ◽  
Kyoungtae Kim
Keyword(s):  
Carbon Nanotubes ◽  
Quantum Dots ◽  
High Throughput Sequencing ◽  
The Body ◽  
Rna Seq ◽  
Mechanisms Of Toxicity ◽  
Promising Tool ◽  
Engineered Nanomaterial ◽  
Next Generation Sequencing Ngs ◽  
Transcriptomic Changes

Next-generation sequencing (NGS) technology has revolutionized sequence-based research. In recent years, high-throughput sequencing has become the method of choice in studying the toxicity of chemical agents through observing and measuring changes in transcript levels. Engineered nanomaterial (ENM)-toxicity has become a major field of research and has adopted microarray and newer RNA-Seq methods. Recently, nanotechnology has become a promising tool in the diagnosis and treatment of several diseases in humans. However, due to their high stability, they are likely capable of remaining in the body and environment for long periods of time. Their mechanisms of toxicity and long-lasting effects on our health is still poorly understood. This review explores the effects of three ENMs including carbon nanotubes (CNTs), quantum dots (QDs), and Ag nanoparticles (AgNPs) by cross examining publications on transcriptomic changes induced by these nanomaterials.

scholarly journals Differential Expression Analysis of Phytohormone-Related Genes of Korean Wheat (Triticum aestivum) in Response to Preharvest Sprouting and Abscisic Acid (ABA)

2021 ◽  
Vol 11 (8) ◽  
pp. 3562
Author(s):  
Yong Jin Lee ◽  
Sang Yong Park ◽  
Dae Yeon Kim ◽  
Jae Yoon Kim
Keyword(s):  
Abscisic Acid ◽  
Differential Expression Analysis ◽  
Preharvest Sprouting ◽  
Global Changes ◽  
Rna Seq ◽  
Hormone Metabolism ◽  
Global Issue ◽  
End Use ◽  
Transcriptomic Changes

Preharvest sprouting (PHS) is a key global issue in production and end-use quality of cereals, particularly in regions where the rainfall season overlaps the harvest. To investigate transcriptomic changes in genes affected by PHS-induction and ABA-treatment, RNA-seq analysis was performed in two wheat cultivars that differ in PHS tolerance. A total of 123 unigenes related to hormone metabolism and signaling for abscisic acid (ABA), gibberellic acid (GA), indole-3-acetic acid (IAA), and cytokinin were identified and 1862 of differentially expressed genes were identified and divided into 8 groups by transcriptomic analysis. DEG analysis showed the majority of genes were categorized in sugar related processes, which interact with ABA signaling in PHS tolerant cultivar under PHS-induction. Thus, genes related to ABA are key regulators of dormancy and germination. Our results give insight into global changes in expression of plant hormone related genes in response to PHS.

Sign in / Sign up

Export Citation Format

Share Document