Locus heterogeneity in the mechanism underlying the superior fermentation performances of phylogenetically distant sake yeasts.

Sake yeasts, Saccharomyces cerevisiae strains isolated from Japanese sake fermentation tanks, exhibit superior fermentation performance to that of other yeast strains. Although the exceptional abilities of the modern sake yeast strain K701 have been extensively investigated, those of phylogenetically distant classical sake yeasts remain largely understudied. In this study, we aimed to clarify the mechanism underlying the superior fermentation ability of the classical sake yeast strain Km67 by comparing its genetic and physiological properties with those of the laboratory strains X2180 and K701.

Metabolic flux and flux balance analyses indicate the relevance of metabolic thermogenesis and aerobic glycolysis in cancer cells.

Adenosine triphosphate (ATP) regeneration by substrate-level phosphorylation is a general feature of cancer metabolism, even under normoxic conditions (aerobic glycolysis). However, it is unclear why cancer cells prefer inefficient aerobic glycolysis over the highly efficient process of oxidative phosphorylation for ATP regeneration. To investigate the metabolic principles underlying aerobic glycolysis, we performed C-metabolic flux analysis of 12 cultured cancer cell lines and explored the metabolic constraints required to reproduce the results using in silico metabolic simulations.

Metabolic Engineering of the 5-Aminolevulinate Biosynthetic Pathway in E. coli Improves Efficiency of Hemoprotein-Based Biocatalysis.

Biocatalysis using heme-dependent enzymes provides a powerful synthetic platform to facilitate a variety of chemical transformations required for organic synthesis. Despite recent advances in biocatalysis, recombinant expression systems for hemoproteins leave much room for improvement due to the strict regulation of heme biosynthesis in the host organism. To develop an efficient cofactor supplementation system for the expression of active holohemoproteins, we describe metabolic engineering of the heme biosynthetic pathway in E.

ATP Supply from Cytosol to Mitochondria Is an Additional Role of Aerobic Glycolysis to Prevent Programmed Cell Death by Maintenance of Mitochondrial Membrane Potential.

Eukaryotic cells generate ATP primarily via oxidative and substrate-level phosphorylation. Despite the superior efficiency of oxidative phosphorylation, eukaryotic cells often use both pathways as aerobic glycolysis, even in the presence of oxygen. However, its role in cell survival remains poorly understood.

RB1 controls differentiation through positive regulation of phosphoglycerate mutases.

Most glycolytic enzymes are transcriptionally controlled by hypoxia-inducible factor-1α (HIF-1α) and/or MYC, however, phosphoglycerate mutases (PGAMs) are exceptional. Retinoblastoma tumor suppressor 1 (RB1) loss converts poorly spherogenic Trp53-null leiomyosarcoma cells to highly spherogenic. We determined a gene expression signature of RB1 loss-of-function in this setting and identified PGAM2 as a positive transcriptional target of RB1.

Comparative metabolome analysis of sake yeast with enhanced fermentation performance in sake fermentation conditions.

Japanese sake is fermented with specific strains of budding yeast Saccharomyces cerevisiae. Sake yeasts can allow the ethanol concentration of sake to exceed 20 % without distillation. While the genetic mutations responsible for these exceptional properties have been investigated, the underlying metabolism has not been fully explored.

C-metabolic flux analysis of in complex media.

is often cultivated in complex media for applications in food and other biochemical production. However, C-metabolic flux analysis (C-MFA) has been conducted for cultivated in synthetic media, resulting in a limited understanding of the metabolic flux distributions under the complex media. In this study, C-MFA was applied to cultivated in complex media to quantify the metabolic fluxes in the central metabolic network.

Data-independent acquisition-based lipidomics reveals lipidome alterations associated with growth of Saccharomyces cerevisiae at low temperature.

Budding yeast, Saccharomyces cerevisiae, adapts to low-temperature stress by altering the amounts and proportions of phospholipids, as well as the structures of acyl chains. To better understand this process, a data-independent acquisition-based lipidomics using liquid chromatography-quadrupole time-of-flight mass spectrometry method was developed to quantify acyl chain isomers in glycerolipids and phospholipids. This method distinguished lipid molecular species, such as phosphatidylcholine (PC) 16:1_18:0 and PC16:0_18:1, at the level of acyl chain isomers.

ΔΔ Method for Elucidating Key Control Reactions from Relative Quantification Metabolome Data: Comparative Analysis of Yeast Glycolysis.

This study introduces the ΔΔ method, a novel approach to analyzing metabolic regulation using relative quantification metabolome data. The method calculates shifts in the Gibbs free energy change (Δ) in two different metabolic states. Subsequently, key reactions controlling the metabolic flux can be identified by comparing the ΔΔ values to the reaction rates.

Combinatorial Nonribosomal Peptide Synthetase Libraries Using the SEAM-Combi-OGAB Method.

To overcome the difficulty of building large nonribosomal peptide synthetase (NRPS) gene cluster libraries, an efficient one-pot method using was developed. This new method, named eamed xpress ssembly ethod (SEAM)-combi-rdered ene ssembly in (OGAB), combines the SEAM-OGAB approach for NRPS gene cluster construction with the combi-OGAB method for combinatorial DNA library construction to randomly swap DNA fragments for NRPS modules. In this study, NRPS gene clusters of plipastatin and gramicidin S were used as the starting material.

Discovery and identification of a novel yeast species, sp. nov., from in Okinawa, Japan.

, a genus of yeasts in which many species reproduce sexually, has attracted the attention of researchers because of its prevalence in diverse ecological niches. Building on our extensive collection efforts since 2020, three previously unknown yeast strains from wild species trapped in ripe bananas in Okinawa, Japan, were isolated. Using a multifaceted approach, including physiological assessments and sequence analysis of the D1/D2 domain of the 26S LSU rRNA gene and the internal transcribed spacer (ITS) region, it was revealed that these strains are novel members of the genus .

C-metabolic flux analysis of respiratory chain disrupted strain ΔndhF1 of Synechocystis sp. PCC 6803.

Cyanobacteria are advantageous hosts for industrial applications toward achieving sustainable society due to their unique and superior properties such as atmospheric CO fixation via photosynthesis. However, cyanobacterial productivities tend to be weak compared to heterotrophic microbes. To enhance them, it is necessary to understand the fundamental metabolic mechanisms unique to cyanobacteria.

Data Processing of Product Ion Spectra: Methods to Control False Discovery Rate in Compound Search Results for Untargeted Metabolomics.

Several database search methods have been employed in untargeted metabolomics utilizing high-resolution mass spectrometry to comprehensively annotate acquired product ion spectra. Recent technical advancements in analyses have facilitated the sorting of the degree of coincidence between a query product ion spectrum, and the molecular structures in the database. However, certain search results may be false positives, necessitating a method for controlling the false discovery rate (FDR).

sp. nov., a novel yeast species associated with Bengal clock vines and soil in Okinawa, Japan.

Two strains, designated JCM 36746 and JCM 36749, were isolated from Bengal clock vine () and soil, respectively, in Okinawa, Japan. Analysis of the internal transcribed spacer (ITS) regions and D1/D2 domains of the large subunit rRNA gene sequences revealed identical sequences in both strains, indicating that they belong to the same species. Sequence analysis and physiological characterization identified these strains as representing a novel yeast species in the genus .

C-metabolic flux analysis reveals metabolic rewiring in HL-60 neutrophil-like cells through differentiation and immune stimulation.

Neutrophils are innate immune cells and the first line of defense for the maintenance of homeostasis. However, our knowledge of the metabolic rewiring associated with their differentiation and immune stimulation is limited. Here, quantitative C-metabolic flux analysis was performed using HL-60 cells as the neutrophil model.

Metabolome analysis of metabolic burden in Escherichia coli caused by overexpression of green fluorescent protein and delta-rhodopsin.

Overexpression of proteins by introducing a DNA vector is among the most important tools for the metabolic engineering of microorganisms such as Escherichia coli. Protein overexpression imposes a burden on metabolism because metabolic pathways must supply building blocks for protein and DNA synthesis. Different E.

Data Processing of Product Ion Spectra: Redundancy of Product Ion Spectra of Small Molecules in Data-Dependent Acquisition Dataset.

Non-targeted metabolome analysis studies comprehensively acquire product ion spectra from the observed ions by the data-dependent acquisition (DDA) mode of tandem mass spectrometry (MS). A DDA dataset redundantly contains closely similar product ion spectra of metabolites commonly existing among the biological samples analyzed in a metabolome study. Moreover, a single DDA data file often includes two or more closely similar raw spectra obtained from an identical precursor ion.

Improved 2,3-Butanediol Production Rate of Metabolically Engineered by Deletion of and Activation of Pyruvate Consumption Pathway.

is a promising host for the bioproduction of higher alcohols, such as 2,3-butanediol (2,3-BDO). Metabolically engineered strains that produce 2,3-BDO via glycolysis have been constructed. However, the specific 2,3-BDO production rates of engineered strains must be improved.

Lipidome and metabolome analyses reveal metabolic alterations associated with MCF-7 apoptosis upon 4-hydroxytamoxifen treatment.

4-hydroxytamoxifen (OHT) is an anti-cancer drug that induces apoptosis in breast cancer cells. Although changes in lipid levels and mitochondrial respiration have been observed in OHT-treated cells, the overall mechanisms underlying these metabolic alterations are poorly understood. In this study, time-series metabolomics and lipidomics were used to analyze the changes in metabolic profiles induced by OHT treatment in the MCF-7 human breast cancer cell line.

Improvement of ethanol and 2,3-butanediol production in Saccharomyces cerevisiae by ATP wasting.

Background: "ATP wasting" has been observed in C metabolic flux analyses of Saccharomyces cerevisiae, a yeast strain commonly used to produce ethanol. Some strains of S. cerevisiae, such as the sake strain Kyokai 7, consume approximately two-fold as much ATP as laboratory strains.

Effects of n-butanol production on metabolism and the photosystem in Synecococcus elongatus PCC 7942 based on metabolic flux and target proteome analyses.

Although n-butanol (BuOH) is an ideal fuel because of its superior physical properties, it has toxicity to microbes. Previously, a Synechococcus elongatus PCC 7942 derivative strain that produces BuOH from CO was developed by introducing six heterologous genes (BUOH-SE strain). To identify the bottleneck in BuOH production, the effects of BuOH production and its toxicity on central metabolism and the photosystem were investigated.

sp. nov., a novel yeast species isolated from flowers and insects in Japan.

Two strains were isolated from flowers and insects in Japan, namely NBRC 115686 and NBRC 115687, respectively. Based on sequence analysis of the D1/D2 domain of the 26S large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region and physiological characteristics, these strains were found to represent a novel yeast species of the genus . Considering pairwise sequence similarity, NBRC 115686 and NBRC 115687 differ from the type strain of the most closely related species, NRRL Y-17645, by 65-66 nucleotide substitutions with 12 gaps (11.

Data Processing of Product Ion Spectra: Quality Improvement by Averaging Multiple Similar Spectra of Small Molecules.

In metabolomics studies using high-resolution mass spectrometry (MS), a set of product ion spectra is comprehensively acquired from observed ions using the data-dependent acquisition (DDA) mode of various tandem MS. However, especially for low-intensity signals, it is sometimes difficult to distinguish artifact signals from true fragment ions derived from a precursor ion. Inadequate precision in the measured / value is also one of the bottlenecks to narrowing down the candidate compositional formula.