(Un)folding mechanisms of adaptation to ER stress: lessons from aneuploidy

A Colletotrichum fructicola dual specificity phosphatase CfMsg5 is regulated by the CfAp1 transcription factor during oxidative stress and promotes virulence on Camellia oleifera

Anthracnose, caused by Colletotrichum species, induces significant economic damages to crop plants annually, especially for Camellia oleifera. During infection, the counter-defence mechanisms of plant pathogens against ROS-mediated resistance, however, remain poorly understood. By employing Weighted Gene Co-expression Network Analysis (WGCNA), we identified ACTIVATOR PROTEIN-1 (AP-1), a bZIP transcription factor, as significant to infection. And deletion of CfAP1 inhibited aerial hyphae formation and growth under oxidative stress. Furthermore, RNA-seq analysis post H2O2 treatment revealed 33 significantly down-regulated genes in the AP-1 deficient strain, including A12032, a dual specificity phosphatase (DSP) homologous to MSG5 from Saccharomyces cerevisiae. This ΔCfmsg5 strain showed enhanced oxidative tolerance, reduced ROS scavenging, and negative regulation of the CWI MAPK cascade under oxygen stress, suggesting its involvement in oxidative signal transduction. Importantly, we provide evidence that CfMsg5 regulates growth, endoplasmic reticulum stress, and several unfolded protein response genes upregulated in ΔCfmsg5. Collectively, this study identified core components during C. fructicola infection and highlights a potential regulatory module involving CfAp1 and CfMsg5 in response to host ROS bursts. It provides new insights into fungal infection mechanisms and potential targets like CfAP1 and CfMSG5 for managing anthracnose diseases.

Transcriptome Analysis Reveals the Stress Tolerance Mechanisms of Cadmium in Zoysia japonica

Cadmium (Cd) is a severe heavy metal pollutant globally. Zoysia japonica is an important perennial warm-season turf grass that potentially plays a role in phytoremediation in Cd-polluted soil areas; however, the molecular mechanisms underlying its Cd stress response are unknown. To further investigate the early gene response pattern in Z. japonica under Cd stress, plant leaves were harvested 0, 6, 12, and 24 h after Cd stress (400 μM CdCl2) treatment and used for a time-course RNA-sequencing analysis. Twelve cDNA libraries were constructed and sequenced, and high-quality data were obtained, whose mapped rates were all higher than 94%, and more than 601 million bp of sequence were generated. A total of 5321, 6526, and 4016 differentially expressed genes were identified 6, 12, and 24 h after Cd stress treatment, respectively. A total of 1660 genes were differentially expressed at the three time points, and their gene expression profiles over time were elucidated. Based on the analysis of these genes, the important mechanisms for the Cd stress response in Z. japonica were identified. Specific genes participating in glutathione metabolism, plant hormone signal and transduction, members of protein processing in the endoplasmic reticulum, transporter proteins, transcription factors, and carbohydrate metabolism pathways were further analyzed in detail. These genes may contribute to the improvement of Cd tolerance in Z. japonica. In addition, some candidate genes were highlighted for future studies on Cd stress resistance in Z. japonica and other plants. Our results illustrate the early gene expression response of Z. japonica leaves to Cd and provide some new understanding of the molecular mechanisms of Cd stress in Zosia and Gramineae species.

Optogenetic closed-loop feedback control of the unfolded protein response optimizes protein production

In biotechnological protein production processes, the onset of protein unfolding at high gene expression levels leads to diminishing production yields and reduced efficiency. Here we show that in silico closed-loop optogenetic feedback control of the unfolded protein response (UPR) in S. cerevisiae clamps gene expression rates at intermediate near-optimal values, leading to significantly improved product titers. Specifically, in a fully-automated custom-built 1L-photobioreactor, we used a cybergenetic control system to steer the level of UPR in yeast to a desired set-point by optogenetically modulating the expression of α-amylase, a hard-to-fold protein, based on real-time feedback measurements of the UPR, resulting in 60% higher product titers. This proof-of-concept study paves the way for advanced optimal biotechnology production strategies that diverge from and complement current strategies employing constitutive overexpression or genetically hardwired circuits.

Heavy metal exposure induces Yap1 and Hac1 mediated derepression of GSH1 and KAR2 by Tup1-Cyc8 complex

Heavy metal pollution is one of the most severe environmental problem. The toxicity of heavy metals is correlated with the production of increased reactive oxygen species and misfolded protein accumulation. Exposures of these metals even at low concentrations adversely affect human health. The Tup1-Cyc8 complex has been identified as a general repressor complex, is also involved in the derepression of few target genes in association with gene-specific activator proteins. Exposure to heavy metals activates the antioxidant defense mechanism, essential for cellular homeostasis. Here we present evidence that TUP1/CYC8 deleted cells are compromised to tolerate heavy metals exposure. Upon metal-induced oxidative stress, Yeast AP-1p (Yap1) recruits the Tup1-Cyc8 complex to the promoter of oxidative stress response gene GSH1 and derepresses its expression. We also found that the TUP1/CYC8 deficient cells have altered endoplasmic reticulum (ER) homeostasis and fail to activate the unfolded protein response pathway. In response to ER stress, the Tup1-Cyc8 complex, with the help of activated Hac1, binds to the promoter of ER chaperone KAR2 and activates its transcription. Altogether, our findings suggest that the Tup1-Cyc8 complex is crucial for the activation of genes that are involved in the mitigation of oxidative and ER stress during heavy metal exposure.

Autophagy as a molecular target of quercetin underlying its protective effects in human diseases

Autophagy, known as a "self-eating" process, is associated with degradation of aged or damaged components and organelles. Generally, autophagy is a survival mechanism that provides energy during nutritional deprivation. This mechanism plays a remarkable role during the physiological condition by maintaining homeostasis and energy balance and several pathological conditions, particularly neurological disorders. Due to the critical role of autophagy in cancer, much attention has been made in the regulation of autophagy using both naturally occurring and synthetic drugs. Quercetin is a plant-derived chemical belonging to the family of flavonoids. Quercetin has valuable biological and therapeutic effects such as anti-tumor, antioxidant, anti-inflammatory, anti-diabetic, hepatoprotective, and cardioprotective. At the present review, we first provide an introduction about quercetin and autophagy with its related molecular pathways. We also describe how quercetin modulates autophagy mechanism to exert its therapeutic effects.

Burden Imposed by Heterologous Protein Production in Two Major Industrial Yeast Cell Factories: Identifying Sources and Mitigation Strategies

Production of heterologous proteins, especially biopharmaceuticals and industrial enzymes, in living cell factories consumes cellular resources. Such resources are reallocated from normal cellular processes toward production of the heterologous protein that is often of no benefit to the host cell. This competition for resources is a burden to host cells, has a negative impact on cell fitness, and may consequently trigger stress responses. Importantly, this often causes a reduction in final protein titers. Engineering strategies to generate more burden resilient production strains offer sustainable opportunities to increase production and profitability for this growing billion-dollar global industry. We review recently reported impacts of burden derived from resource competition in two commonly used protein-producing yeast cell factories: Saccharomyces cerevisiae and Komagataella phaffii (syn. Pichia pastoris). We dissect possible sources of burden in these organisms, from aspects related to genetic engineering to protein translation and export of soluble protein. We also summarize advances as well as challenges for cell factory design to mitigate burden and increase overall heterologous protein production from metabolic engineering, systems biology, and synthetic biology perspectives. Lastly, future profiling and engineering strategies are highlighted that may lead to constructing robust burden-resistant cell factories. This includes incorporation of systems-level data into mathematical models for rational design and engineering dynamical regulation circuits in production strains.

ALDH2 protects naturally aged mouse retina via inhibiting oxidative stress-related apoptosis and enhancing unfolded protein response in endoplasmic reticulum

During the process of aging, the retina exhibits chronic oxidative stress (OS) damage. Our preliminary experiment showed that acetaldehyde dehydrogenase 2 (ALDH2) could alleviate retinal damage caused by OS. This study aimed to explore whether ALDH2 could inhibit mice retinal cell apoptosis and enhance the function of unfolded protein response in endoplasmic reticulum (UPRER) through reducing OS in aging process. Retinal function and structure in vivo and in vitro were examined in aged ALDH2+ overexpression mice and ALDH2 agonist Alda1-treated aged mice. Levels of ALDH2, endoplasmic reticulum stress (ERS), apoptosis and inflammatory cytokines were evaluated. Higher expression of ALDH2 was observed at the outer nuclear layer (ONL) and the inner nuclear layer (INL) in aged ALDH2+ overexpression and aged Alda1-treated mice. Moreover, aged ALDH2+ overexpression mice and aged Alda1-treated mice exhibited better retinal function and structure. Increased expression of glucose-regulated protein 78 (GRP78) and ERS-related protein phosphorylated eukaryotic initiation factor 2 (peIF2α) and decreased expression of apoptosis-related protein, including C/EBP homologous protein (CHOP), caspase12 and caspase9, and retinal inflammatory cytokines were detected in the retina of aged ALDH2+ overexpression mice and aged Alda1-treated mice. The expression of ALDH2 in the retina was decreased in aging process. ALDH2 could reduce retinal oxidative stress and apoptosis, strengthen UPRER during the aging process to improve retinal function and structure.

The adaptive potential of circular DNA accumulation in ageing cells

Carefully maintained and precisely inherited chromosomal DNA provides long-term genetic stability, but eukaryotic cells facing environmental challenges can benefit from the accumulation of less stable DNA species. Circular DNA molecules lacking centromeres segregate randomly or asymmetrically during cell division, following non-Mendelian inheritance patterns that result in high copy number instability and massive heterogeneity across populations. Such circular DNA species, variously known as extrachromosomal circular DNA (eccDNA), microDNA, double minutes or extrachromosomal DNA (ecDNA), are becoming recognised as a major source of the genetic variation exploited by cancer cells and pathogenic eukaryotes to acquire drug resistance. In budding yeast, circular DNA molecules derived from the ribosomal DNA (ERCs) have been long known to accumulate with age, but it is now clear that aged yeast also accumulate other high-copy protein-coding circular DNAs acquired through both random and environmentally-stimulated recombination processes. Here, we argue that accumulation of circular DNA provides a reservoir of heterogeneous genetic material that can allow rapid adaptation of aged cells to environmental insults, but avoids the negative fitness impacts on normal growth of unsolicited gene amplification in the young population.

Mechanisms by which PE21, an extract from the white willow Salix alba, delays chronological aging in budding yeast

We have recently found that PE21, an extract from the white willow Salix alba, slows chronological aging and prolongs longevity of the yeast Saccharomyces cerevisiae more efficiently than any of the previously known pharmacological interventions. Here, we investigated mechanisms through which PE21 delays yeast chronological aging and extends yeast longevity. We show that PE21 causes a remodeling of lipid metabolism in chronologically aging yeast, thereby instigating changes in the concentrations of several lipid classes. We demonstrate that such changes in the cellular lipidome initiate three mechanisms of aging delay and longevity extension. The first mechanism through which PE21 slows aging and prolongs longevity consists in its ability to decrease the intracellular concentration of free fatty acids. This postpones an age-related onset of liponecrotic cell death promoted by excessive concentrations of free fatty acids. The second mechanism of aging delay and longevity extension by PE21 consists in its ability to decrease the concentrations of triacylglycerols and to increase the concentrations of glycerophospholipids within the endoplasmic reticulum membrane. This activates the unfolded protein response system in the endoplasmic reticulum, which then decelerates an age-related decline in protein and lipid homeostasis and slows down an aging-associated deterioration of cell resistance to stress. The third mechanisms underlying aging delay and longevity extension by PE21 consists in its ability to change lipid concentrations in the mitochondrial membranes. This alters certain catabolic and anabolic processes in mitochondria, thus amending the pattern of aging-associated changes in several key aspects of mitochondrial functionality.

Co-Operation between Aneuploidy and Metabolic Changes in Driving Tumorigenesis

Alterations from the normal set of chromosomes are extremely common as cells progress toward tumourigenesis. Similarly, we expect to see disruption of normal cellular metabolism, particularly in the use of glucose. In this review, we discuss the connections between these two processes: how chromosomal aberrations lead to metabolic disruption, and vice versa. Both processes typically result in the production of elevated levels of reactive oxygen species, so we particularly focus on their role in mediating oncogenic changes.

The P5-type ATPase Spf1 is required for development and virulence of the rice blast fungus Pyricularia oryzae

Pyricularia oryzae (synonym Magnaporthe oryzae) is a plant pathogen causing major yield losses in cultivated rice and wheat. The P-type ATPases play important roles in cellular processes of fungi, plants, and animals via transporting specific substrates through ATP hydrolysis. Here, we characterized the roles of a P5-ATPase, Spf1, in the development and virulence of P. oryzae. Deletion of SPF1 led to decreased hyphal growth and conidiation, delayed spore germination and appressorium formation, reduced penetration and invasive hyphal extension, and attenuated virulence. Appressorium turgor, however, was not affected by deletion of SPF1. The co-localization of Spf1-GFP and an endoplasmic reticulum (ER) marker protein, Lhs1-DsRed2, indicated that Spf1 is an ER-localized P5-ATPase. An ER stress factor, 0.5 μg/ml tunicamycin (TUNI), inhibited the growth of ∆spf1, but another ER stress factor, 5 mM dithiothreitol (DTT), promoted the growth of ∆spf1. Treatment with chemicals for oxidative stress (5 mM H₂O₂ and 0.8 mM paraquat) also promoted the growth of ∆spf1. Gene expression assays showed that unfolded protein response (UPR) components KAR2, OST1, PMT1, ERV29, PDI1, SCJ1, SEC61, a Ca²⁺ channel-related P-type ATPase gene PMR1, and a calcineurin-dependent transcription factor CRZ1 were significantly up-regulated in ∆spf1, suggesting activation of UPR in the mutant. These lines of experimental evidence indicate that SPF1 is involved in some basal ER mechanisms of P. oryzae including UPR pathway and responses to ER related stresses, therefore, affecting fungal development and virulence. However, the detailed mechanism between Spf1 and virulence still awaits future researches.

A functional unfolded protein response is required for chronological aging in Saccharomyces cerevisiae

Progressive impairment of proteostasis and accumulation of toxic misfolded proteins are associated with the cellular aging process. Here, we employed chronologically aged yeast cells to investigate how activation of the unfolded protein response (UPR) upon accumulation of misfolded proteins in the endoplasmic reticulum (ER) affects lifespan. We found that cells lacking a functional UPR display a significantly reduced chronological lifespan, which contrasts previous findings in models of replicative aging. We find exacerbated UPR activation in aged cells, indicating an increase in misfolded protein burden in the ER during the course of aging. We also observed that caloric restriction, which promotes longevity in various model organisms, extends lifespan of UPR-deficient strains. Similarly, aging in pH-buffered media extends lifespan, albeit independently of the UPR. Thus, our data support a role for caloric restriction and reduced acid stress in improving ER homeostasis during aging. Finally, we show that UPR-mediated upregulation of the ER chaperone Kar2 and functional ER-associated degradation (ERAD) are essential for proper aging. Our work documents the central role of secretory protein homeostasis in chronological aging in yeast and highlights that the requirement for a functional UPR can differ between post-mitotic and actively dividing eukaryotic cells.