Dynamics of the Heat Stress Response of Ceramides with Different Fatty-Acyl Chain Lengths in Baker's Yeast

Mechanism of enhanced salt tolerance in Saccharomyces cerevisiae by CRZ1 overexpression

Achieving high-gravity fermentation in the industrial production of fuel ethanol, and enhancing the fermentation efficiency of high-salt raw materials, such as waste molasses, can significantly reduce wastewater output and process costs. Therefore, the development of hyperosmotic-tolerant industrial Saccharomyces cerevisiae strains, capable of resisting high-salt stress, offers both environmental and economic benefits. Our previous study highlighted the potential of CRZ1 overexpression as a strategy to improve the yeast strain's resistance to high-salt stress, however, the underlying molecular mechanisms remain unexplored. The fermentation capabilities of the CRZ1-overexpressing strain, KCR3, and its parental strain, KF7, were evaluated under condition of 1.25 M NaCl at 35 °C. Compared to KF7, KCR3 showed an 81% increase in glucose consumption (129.25 ± 0.83 g/L) and a 105% increase in ethanol production (47.59 ± 0.93 g/L), with a yield of 0.37 g/g. Comparative transcriptomic analysis showed that under high-salt stress, KCR3 exhibited significantly upregulated expression of genes associated with ion transport, stress response, gluconeogenesis, and the utilization of alternative carbon sources, while genes related to glycolysis and the biosynthesis of ribosomes, amino acids, and fatty acids were notably downregulated compared to KF7. Crz1 likely expands its influence by regulating the expression of numerous transcription factors, thereby impacting genes involved in multiple aspects of cellular function. The study revealed the regulatory mechanism of Crz1 under high-salt stress, thereby providing guidance for the construction of salt-tolerant strains.

Ceramide sorting into non-vesicular transport is independent of acyl chain length in budding yeast

The transport of ceramide from the endoplasmic reticulum (ER) to the Golgi is a key step in the synthesis of complex sphingolipids, the main building blocks of the plasma membrane. In yeast, ceramide is transported to the Golgi either through ATP-dependent COPII vesicles of the secretory pathway or by ATP-independent non-vesicular transport that involves tethering proteins at ER-Golgi membrane contact sites. Studies in both mammalian and yeast cells reported that vesicular transport mainly carries ceramide containing very long chain fatty acids, while the main mammalian non-vesicular ceramide transport protein CERT only transports ceramides containing short chain fatty acids. However, if non-vesicular ceramide transport in yeast similarly favors short chain ceramides remained unanswered. Here we employed a yeast GhLag1 strain in which the endogenous ceramide synthase is replaced by the cotton-derived GhLag1 gene, resulting in the production of short chain C18 rather than C26 ceramides. We show that block of vesicular transport through ATP-depletion or the use of temperature-sensitive sec mutants caused a reduction in inositolphosphorylceramide (IPC) synthesis to similar extent in WT and GhLag1 backgrounds. Since the remaining IPC synthesis is a readout for non-vesicular ceramide transport, our results indicate that non-vesicular ceramide transport is neither blocked nor facilitated when only short chain ceramides are present. Therefore, we propose that the sorting of ceramide into non-vesicular transport is independent of acyl chain length in budding yeast.

The fatty acid 2-hydroxylase CsSCS7 is a key hyphal growth factor and potential control target in Colletotrichum siamense

SCS7 is a fatty acid 2-hydroxylase required for the synthesis of inositol phosphorylceramide but is not essential for normal growth in Saccharomyces cerevisiae. Here, we demonstrate that the Colletotrichum siamense SCS7 homolog CsSCS7 plays a key role in hyphal growth. The CsSCS7 deletion mutant showed strong hyphal growth inhibition, small conidia, and marginally reduced sporulation and also resulted in a sharp reduction in the full virulence and increasing the fungicide sensitivity. The three protein domains (a cytochrome b5 domain, a transmembrane domain, and a hydroxylase domain) are important to CsSCS7 protein function in hyphal growth. The fatty acid assay results revealed that the CsSCS7 gene is important for balancing the contents of multiple mid-long- and short-chain fatty acids. Additionally, the retarded growth and virulence of C. siamense ΔCsSCS7 can be recovered partly by the reintroduction of homologous sequences from Magnaporthe oryzae and Fusarium graminearum but not SCS7 of S. cerevisiae. In addition, the spraying of C. siamense with naked CsSCS7-double-stranded RNA (dsRNAs), which leads to RNAi, increases the inhibition of hyphal growth and slightly decreases disease lesions. Then, we used nano material Mg-Al-layered double hydroxide as carriers to deliver dsRNA, which significantly enhanced the control effect of dsRNA, and the lesion area was obviously reduced. These data indicated that CsSCS7 is an important factor for hyphal growth and affects virulence and may be a potential control target in C. siamense and even in filamentous plant pathogenic fungi.IMPORTANCECsSCS7, which is homologous to yeast fatty acid 2-hydroxylase SCS7, was confirmed to play a key role in the hyphal growth of Colletotrichum siamense and affect its virulence. The CsSCS7 gene is involved in the synthesis and metabolism of fatty acids. Homologs from the filamentous fungi Magnaporthe oryzae and Fusarium graminearum can recover the retarded growth and virulence of C. siamense ΔCsSCS7. The spraying of double-stranded RNAs targeting CsSCS7 can inhibit hyphal growth and reduce the disease lesion area to some extent. After using nano material Mg-Al layered double hydroxide as carrier, the inhibition rates were significantly increased. We demonstrated that CsSCS7 is an important factor for hyphal growth and affects virulence and may be a potential control target in C. siamense and even in filamentous plant pathogenic fungi.

Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions

The Sc2.0 project is building a eukaryotic synthetic genome from scratch. A major milestone has been achieved with all individual Sc2.0 chromosomes assembled. Here, we describe the consolidation of multiple synthetic chromosomes using advanced endoreduplication intercrossing with tRNA expression cassettes to generate a strain with 6.5 synthetic chromosomes. The 3D chromosome organization and transcript isoform profiles were evaluated using Hi-C and long-read direct RNA sequencing. We developed CRISPR Directed Biallelic URA3-assisted Genome Scan, or "CRISPR D-BUGS," to map phenotypic variants caused by specific designer modifications, known as "bugs." We first fine-mapped a bug in synthetic chromosome II (synII) and then discovered a combinatorial interaction associated with synIII and synX, revealing an unexpected genetic interaction that links transcriptional regulation, inositol metabolism, and tRNASerCGA abundance. Finally, to expedite consolidation, we employed chromosome substitution to incorporate the largest chromosome (synIV), thereby consolidating >50% of the Sc2.0 genome in one strain.

Hepatic cholesterol biosynthesis and dioxin-induced dysregulation: A multiscale computational approach

Humans are constantly exposed to lipophilic persistent organic pollutants (POPs) that accumulate in fatty foods. Among the numerous POPs, dioxins, in particular 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), can impact several organ systems. While the hazard is clearly recognized, it is still difficult to develop a comprehensive understanding of the overall health impacts of dioxins. As chemical toxicity testing is steadily adopting new approach methodologies (NAMs), it becomes imperative to develop computational models that can bridge the data gaps between in vitro testing and in vivo outcomes. As an effort to address this challenge, we propose a multiscale computational approach using a "template-and-anchor" (T&A) structure. A template is a high-level umbrella model that permits the integration of information from various, detailed anchor models. In the present study, we use this T&A approach to describe the effect of TCDD on cholesterol dynamics. Specifically, we represent hepatic cholesterol biosynthesis as an anchor model that is perturbed by TCDD, leading to steatosis, along with alterations of plasma cholesterol. In the future, incorporating pertinent information from all anchor models into the template model will allow the characterization of the global effects of dioxin, which can subsequently be translated into overall - and ultimately personalized - human health risk assessment.

Thermal protection function of camphor on Cinnamomum camphora cell membrane by acting as a signaling molecule

Isoprenoids serve important functions in protecting plant membranes against high temperature. Cinnamomum camphora is an excellent economic tree species, and releases plenty of monoterpenes. To uncover the protective mechanism of monoterpenes on the membrane system for promoting their development and utilization as anti-high temperature agents, the membrane permeability, cell ultrastructure, membrane lipid variations and related gene expression were investigated in C. camphora fumigated with camphor, one of the main monoterpenes in the plant, after fosmidomycin (Fos) blocking the monoterpene biosynthesis under high temperature (Fos+38 °C + C). High temperature at 38 °C caused the rupture of plasma as well as chloroplast and mitochondrion membranes, deformation of chloroplasts and mitochondria, and electrolyte leakage in C. camphora. High temperature with Fos treatment (Fos+38 °C) aggravated the damage, while camphor fumigation (Fos+38 °C + C) showed alleviating effects. High temperature at 38 °C disturbed the membrane lipid equilibrium by reducing the levels of 14 phosphatidylcholine, 8 phosphatidylglycerol and 6 phosphatidylethanolamine molecules, and increasing the levels of 8 phosphatidic acid, 4 diacylglycerol, 5 phosphatidylinositol, 16 sphingomyelin and 5 ceramide phosphoethanolamine molecules. Fos+38 °C treatment primarily exhibited intensifying effects on the disturbance, while these membrane lipid levels in Fos+38 °C + C5 (5 μM camphor) treatment exhibited variation tendencies to the control at 28 °C. This should result from the expression alterations of the genes related with phospholipid biosynthesis, fatty acid metabolism, and sphingolipid metabolism. It can be speculated that camphor can maintain membrane lipid stabilization in C. camphora under high temperature by acting as a signaling molecule.

The dynamics and role of sphingolipids in eukaryotic organisms upon thermal adaptation

All living beings have an optimal temperature for growth and survival. With the advancement of global warming, the search for understanding adaptive processes to climate changes has gained prominence. In this context, all living beings monitor the external temperature and develop adaptive responses to thermal variations. These responses ultimately change the functioning of the cell and affect the most diverse structures and processes. One of the first structures to detect thermal variations is the plasma membrane, whose constitution allows triggering of intracellular signals that assist in the response to temperature stress. Although studies on this topic have been conducted, the underlying mechanisms of recognizing thermal changes and modifying cellular functioning to adapt to this condition are not fully understood. Recently, many reports have indicated the participation of sphingolipids (SLs), major components of the plasma membrane, in the regulation of the thermal stress response. SLs can structurally reinforce the membrane or/and send signals intracellularly to control numerous cellular processes, such as apoptosis, cytoskeleton polarization, cell cycle arresting and fungal virulence. In this review, we discuss how SLs synthesis changes during both heat and cold stresses, focusing on fungi, plants, animals and human cells. The role of lysophospholipids is also discussed.

Sphingolipids: Regulators of azole drug resistance and fungal pathogenicity

In recent years, the role of sphingolipids in pathogenic fungi, in terms of pathogenicity and resistance to azole drugs, has been a rapidly growing field. This review describes evidence about the roles of sphingolipids in azole resistance and fungal virulence. Sphingolipids can serve as signaling molecules that contribute to azole resistance through modulation of the expression of drug efflux pumps. They also contribute to azole resistance by participating in various microbial pathways such as the unfolded protein response (UPR), pH-responsive Rim pathway, and pleiotropic drug resistance (PDR) pathway. In addition, sphingolipid signaling and eisosomes also coordinately regulate sphingolipid biosynthesis in response to azole-induced membrane stress. Sphingolipids are important for fungal virulence, playing roles during growth in hosts under stressful conditions, maintenance of cell wall integrity, biofilm formation, and production of various virulence factors. Finally, we discuss the possibility of exploiting fungal sphingolipids for the development of new therapeutic strategies to treat infections caused by pathogenic fungi.

Quantitative Operating Principles of Yeast Metabolism during Adaptation to Heat Stress

Microorganisms evolved adaptive responses to survive stressful challenges in ever-changing environments. Understanding the relationships between the physiological/metabolic adjustments allowing cellular stress adaptation and gene expression changes being used by organisms to achieve such adjustments may significantly impact our ability to understand and/or guide evolution. Here, we studied those relationships during adaptation to various stress challenges in Saccharomyces cerevisiae, focusing on heat stress responses. We combined dozens of independent experiments measuring whole-genome gene expression changes during stress responses with a simplified kinetic model of central metabolism. We identified alternative quantitative ranges for a set of physiological variables in the model (production of ATP, trehalose, NADH, etc.) that are specific for adaptation to either heat stress or desiccation/rehydration. Our approach is scalable to other adaptive responses and could assist in developing biotechnological applications to manipulate cells for medical, biotechnological, or synthetic biology purposes.

Mild heat induces a distinct "eustress" response in Chinese Hamster Ovary cells but does not induce heat shock protein synthesis

The current research on cellular heat stress management focuses on the roles of heat shock proteins (HSPs) and the proteostasis network under severe stress conditions. The mild, fever-type stress and the maintenance of membrane homeostasis are less well understood. Herein, we characterized the acute effect of mild, fever-range heat shock on membrane organization, and HSP synthesis and localization in two mammalian cell lines, to delineate the role of membranes in the sensing and adaptation to heat. A multidisciplinary approach combining ultrasensitive fluorescence microscopy and lipidomics revealed the molecular details of novel cellular “eustress”, when cells adapt to mild heat by maintaining membrane homeostasis, activating lipid remodeling, and redistributing chaperone proteins. Notably, this leads to acquired thermotolerance in the complete absence of the induction of HSPs. At higher temperatures, additional defense mechanisms are activated, including elevated expression of molecular chaperones, contributing to an extended stress memory and acquired thermotolerance.

Metabolic systems modeling for cell factories improvement

Techniques for modeling microbial bioproduction systems have evolved over many decades. Here, we survey recent literature and focus on modeling approaches for improving bioproduction. These techniques from systems biology are based on different methodologies, starting from stoichiometry only to various stoichiometry with kinetics approaches that address different issues in metabolic systems. Techniques to overcome unknown kinetic parameters using random sampling have emerged to address meaningful questions. Among those questions, pathway robustness seems to be an important issue for metabolic engineering. We also discuss the increasing significance of databases in biology and their potential impact for biotechnology.

Analysis of the Involvement of Different Ceramide Variants in the Response to Hydroxyurea Stress in Baker's Yeast

Sphingolipids have been identified as important signaling compounds in stress responses. However, it is not always clear how different sphingolipid profiles are achieved in a particular stress situation. Here we propose a detailed mass action model, containing 42 dependent variables and 137 reactions, that offers explanations of the roles of variant ceramides species, which differ in the lengths of their fatty acyl chains and their saturation state, in the response to hydroxyurea stress. The simulations demonstrate that the cells manage to achieve hydroxyurea tolerance through a well-coordinated, differential usage of the variant ceramide species. Moreover, the results suggest that key enzymes have different affinities toward saturated and unsaturated fatty acyl chains, which implies that the saturation state affords the cells with an additional mode of regulation that had not been recognized so far. These conclusions from our computational analysis are yet to be validated experimentally.