Stress-induced growth rate reduction restricts metabolic resource utilization to modulate osmo-adaptation time

Dual regulation of the levels and function of Start transcriptional repressors drives G1 arrest in response to cell wall stress

BACKGROUND

Many different stress signaling pathways converge in a common response: slowdown or arrest cell cycle in the G1 phase. The G1/S transition (called Start in budding yeast) is a key checkpoint controlled by positive and negative regulators. Among them, Whi7 and Whi5 are transcriptional repressors of the G1/S transcriptional program, yeast functional homologs of the Retinoblastoma family proteins in mammalian cells. Under standard conditions, Whi7 plays a lesser role than Whi5 in Start inhibition. However, under cell wall stress, Whi7 is induced and plays a more important role in G1/S control. In this work, we investigated the functional hallmarks of Whi7 and Whi5, which determine their strength as Start inhibitors under cell wall stress.

METHODS

The response of Saccharomyces cerevisiae to Calcofluor White was investigated to characterize the regulation and function of Whi7 and Whi5 under cell wall stress. To control their protein levels, we used dose-dependent β-estradiol-induced expression and auxin-induced degron protein fusions. We also performed Chromatin Immunoprecipitation assays to investigate Whi7 and Whi5 association with Start promoters and scored cell cycle arrest and re-entry using cell microscopy assays.

RESULTS

We found that cell wall stress promoted the specific upregulation of the Whi7 Start repressor. First, although cell wall stress increases Whi7 protein levels, this is not the only determinant behind the Whi7 function in promoting G1 arrest. Indeed, artificial induction of Whi5 at the same protein level resulted in a lower G1 block. Second, under cell wall stress, Whi7 was specifically recruited to SBF-target promoters, independent of the increase in its protein levels or cell cycle stage. Finally, we found that Whi7 protein instability further increased during cell wall stress and that Whi7 degradation triggered advanced cell cycle re-entry.

CONCLUSIONS

Here, we show that cell wall stress signaling specifically enhances Whi7 function as a Start transcriptional repressor. Importantly, we identified new Whi7-specific regulatory mechanisms that do not operate in the Whi5 repressor. Our results indicate that cells may benefit from stress-specific repressors to ensure the stress-induced G1 arrest and that Whi7 rapid degradation may be particularly important to resume cell cycle upon adaptation.

Calcineurin promotes adaptation to chronic stress through two distinct mechanisms

Adaptation to environmental stress requires coordination between stress-defense programs and cell cycle progression. The immediate response to many stressors has been well characterized, but how cells survive in challenging environments long term is unknown. Here, we investigate the role of the stress-activated phosphatase calcineurin (CN) in adaptation to chronic CaCl2 stress in Saccharomyces cerevisiae. We find that prolonged exposure to CaCl2 impairs mitochondrial function and demonstrate that cells respond to this stressor using two CN-dependent mechanisms-one that requires the downstream transcription factor Crz1 and another that is Crz1 independent. Our data indicate that CN maintains cellular fitness by promoting cell cycle progression and preventing CaCl2-induced cell death. When Crz1 is present, transient CN activation suppresses cell death and promotes adaptation despite high levels of mitochondrial loss. However, in the absence of Crz1, prolonged activation of CN prevents mitochondrial loss and further cell death by upregulating glutathione biosynthesis genes thereby mitigating damage from reactive oxygen species. These findings illustrate how cells maintain long-term fitness during chronic stress and suggest that CN promotes adaptation in challenging environments by multiple mechanisms.

Bulk and selective autophagy cooperate to remodel a fungal proteome in response to changing nutrient availability

Cells remodel their proteomes in response to changing environments by coordinating changes in protein synthesis and degradation. In yeast, such degradation involves both proteasomal and vacuolar activity, with a mixture of bulk and selective autophagy delivering many of the vacuolar substrates. Although these pathways are known to be generally important for such remodeling, their relative contributions have not been reported on a proteome-wide basis. To assess this, we developed a method to pulse-label the methylotrophic yeast Komagataella phaffii (i.e. Pichia pastoris) with isotopically labeled nutrients, which, when coupled to quantitative proteomics, allowed us to globally monitor protein degradation on a protein-by-protein basis following an environmental perturbation. Using genetic ablations, we found that a targeted combination of bulk and selective autophagy drove the vast majority of the observed proteome remodeling activity, with minimal non-autophagic contributions. Cytosolic proteins and protein complexes, including ribosomes, were degraded via Atg11-independent bulk autophagy, whereas proteins targeted to the peroxisome and mitochondria were primarily degraded in an Atg11-dependent manner. Notably, these degradative pathways were independently regulated by environmental cues. Taken together, our new approach greatly increases the range of known autophagic substrates and highlights the outsized impact of autophagy on proteome remodeling. Moreover, the resulting datasets, which we have packaged in an accessible online database, constitute a rich resource for identifying proteins and pathways involved in fungal proteome remodeling.

Dynamic phosphorylation of Hcm1 promotes fitness in chronic stress

Cell survival depends upon the ability to adapt to changing environments. Environmental stressors trigger an acute stress response program that rewires cell physiology, downregulates proliferation genes and pauses the cell cycle until the cell adapts. Here, we show that dynamic phosphorylation of the yeast cell cycle-regulatory transcription factor Hcm1 is required to maintain fitness in chronic stress. Hcm1 is activated by cyclin dependent kinase (CDK) and inactivated by the phosphatase calcineurin (CN) in response to stressors that signal through increases in cytosolic Ca2+. Expression of a constitutively active, phosphomimetic Hcm1 mutant reduces fitness in stress, suggesting Hcm1 inactivation is required. However, a comprehensive analysis of Hcm1 phosphomutants revealed that Hcm1 activity is also important to survive stress, demonstrating that Hcm1 activity must be toggled on and off to promote gene expression and fitness. These results suggest that dynamic control of cell cycle regulators is critical for survival in stressful environments.

An integrative temperature-controlled microfluidic system for budding yeast heat shock response analysis at the single-cell level

Cells can respond and adapt to complex forms of environmental change. Budding yeast is widely used as a model system for these stress response studies. In these studies, the precise control of the environment with high temporal resolution is most important. However, there is a lack of single-cell research platforms that enable precise control of the temperature and form of cell growth. This has hindered our understanding of cellular coping strategies in the face of diverse forms of temperature change. Here, we developed a novel temperature-controlled microfluidic platform that integrates a microheater (using liquid metal) and a thermocouple (liquid metal vs. conductive PDMS) on a chip. Three forms of temperature changes (step, gradient, and periodical oscillations) were realized by automated equipment. The platform has the advantages of low cost and a simple fabrication process. Moreover, we investigated the nuclear entry and exit behaviors of the transcription factor Msn2 in yeast in response to heat stress (37 °C) with different heating modes. The feasibility of this temperature-controlled platform for studying the protein dynamic behavior of yeast cells was demonstrated.

Yeast cell responses and survival during periodic osmotic stress are controlled by glucose availability

Natural environments of living organisms are often dynamic and multifactorial, with multiple parameters fluctuating over time. To better understand how cells respond to dynamically interacting factors, we quantified the effects of dual fluctuations of osmotic stress and glucose deprivation on yeast cells using microfluidics and time-lapse microscopy. Strikingly, we observed that cell proliferation, survival, and signaling depend on the phasing of the two periodic stresses. Cells divided faster, survived longer, and showed decreased transcriptional response when fluctuations of hyperosmotic stress and glucose deprivation occurred in phase than when the two stresses occurred alternatively. Therefore, glucose availability regulates yeast responses to dynamic osmotic stress, showcasing the key role of metabolic fluctuations in cellular responses to dynamic stress. We also found that mutants with impaired osmotic stress response were better adapted to alternating stresses than wild-type cells, showing that genetic mechanisms of adaptation to a persistent stress factor can be detrimental under dynamically interacting conditions.

Calcineurin promotes adaptation to chronic stress through two distinct mechanisms

Adaptation to environmental stress requires coordination between stress-defense programs and cell cycle progression. The immediate response to many stressors has been well characterized, but how cells survive in challenging environments long-term is unknown. Here, we investigate the role of the stress-activated phosphatase calcineurin (CN) in adaptation to chronic CaCl2 stress in Saccharomyces cerevisiae. We find that prolonged exposure to CaCl2 impairs mitochondrial function and demonstrate that cells respond to this stressor using two CN-dependent mechanisms - one that requires the downstream transcription factor Crz1 and another that is Crz1-independent. Our data indicate that CN maintains cellular fitness by promoting cell cycle progression and preventing CaCl2-induced cell death. When Crz1 is present, transient CN activation suppresses cell death and promotes adaptation despite high levels of mitochondrial loss. However, in the absence of Crz1, prolonged activation of CN prevents mitochondrial loss and further cell death by upregulating glutathione (GSH) biosynthesis genes thereby mitigating damage from reactive oxygen species. These findings illustrate how cells maintain long-term fitness during chronic stress and suggest that CN promotes adaptation in challenging environments by multiple mechanisms.

Ocular Surface Allostasis-When Homeostasis Is Lost: Challenging Coping Potential, Stress Tolerance, and Resilience

The loss of ocular surface (OS) homeostasis characterizes the onset of dry eye disease. Resilience defines the ability to withstand this threat, reflecting the ability of the ocular surface to cope with and bounce back after challenging events. The coping capacity of the OS defines the ability to successfully manage cellular stress. Cellular stress, which is central to the outcome of the pathophysiology of dry eye disease, is characterized by intensity, continuity, and receptivity, which lead to the loss of homeostasis, resulting in a phase of autocatalytic dysregulation, an event that is not well-defined. To better define this event, here, we present a model providing a potential approach when homeostasis is challenged and the coping capacities have reached their limits, resulting in the stage of heterostasis, in which the dysregulated cellular stress mechanisms take over, leading to dry eye disease. The main feature of the proposed model is the concept that, prior to the initiation of the events leading to cellular stress, there is a period of intense activation of all available coping mechanisms preventing the imminent dysregulation of ocular surface homeostasis. When the remaining coping mechanisms and resilience potential have been maximally exploited and have, finally, been exceeded, there will be a transition to manifest disease with all the well-known signs and symptoms, with a shift to allostasis, reflecting the establishment of another state of balance. The intention of this review was to show that it is possibly the phase of heterostasis preceding the establishment of allostasis that offers a better chance for therapeutic intervention and optimized recovery. Once allostasis has been established, as a new steady-state of balance at a higher level of constant cell stress and inflammation, treatment may be far more difficult, and the potential for reversal is drastically decreased. Homeostasis, once lost, can possibly not be fully recovered. The processes established during heterostasis and allostasis require different approaches and treatments for their control, indicating that the current treatment options for homeostasis need to be adapted to a more-demanding situation. The loss of homeostasis necessarily implies the establishment of a new balance; here, we refer to such a state as allostasis.

The regulatory mechanism of the yeast osmoresponse under different glucose concentrations

Cells constantly respond to environmental changes by modulating gene expression programs. These responses may demand substantial costs and, thus, affect cell growth. Understanding the regulation of these processes represents a key question in biology and biotechnology. Here, we studied the responses to osmotic stress in glucose-limited environments. By analyzing seventeen osmotic stress-induced genes and stress-activated protein kinase Hog1, we found that cells exhibited stronger osmotic gene expression response and larger integral of Hog1 nuclear localization during adaptation to osmotic stress under glucose-limited conditions than under glucose-rich conditions. We proposed and verified that in glucose-limited environment, glycolysis intermediates (representing "reserve flux") were limited, which required cells to express more glycerol-production enzymes for stress adaptation. Consequently, the regulatory mechanism of osmoresponse was derived in the presence and absence of such reserve flux. Further experiments suggested that this reserve flux-dependent stress-defense strategy may be a general principle under nutrient-limited environments.

Chronic Hyperglycemia Compromises Mitochondrial Function in Corneal Epithelial Cells: Implications for the Diabetic Cornea

Mitochondrial dysfunction is a major pathophysiological event leading to the onset of diabetic complications. This study investigated the temporal effects of hyperglycemia on mitochondrial metabolism in corneal epithelial cells. To accomplish this, human telomerase-immortalized corneal epithelial cells were cultured in a defined growth medium containing 6 mM glucose. To simulate hyperglycemia, cells were cultured in a medium containing 25 mM D-glucose, and control cells were cultured in mannitol. Using metabolic flux analysis, there was a hyperosmolar-mediated increase in mitochondrial respiration after 24 h. By day 5, there was a decrease in spare respiratory capacity in cells subject to high glucose that remained suppressed throughout the 14-day period. Although respiration remained high through day 9, glycolysis was decreased. Mitochondrial respiration was decreased by day 14. This was accompanied by the restoration of glycolysis to normoglycemic levels. These changes paralleled a decrease in mitochondrial polarization and cell cycle arrest. Together, these data show that chronic but not acute hyperglycemic stress leads to mitochondrial dysfunction. Moreover, the hyperglycemia-induced loss of spare respiratory capacity reduces the ability of corneal epithelial cells to respond to subsequent stress. Compromised mitochondrial function represents a previously unexplored mechanism that likely contributes to corneal complications in diabetes.

Cip1 tunes cell cycle arrest duration upon calcineurin activation

SignificanceTo ensure their survival, cells arrest the cell division cycle when they are exposed to environmental stress. The duration of this arrest is dependent upon the time it takes a cell to adapt to a particular environment. How cells adjust the amount of time they remain arrested is not known. This study investigates the role of the phosphatase calcineurin in controlling cell cycle arrest duration in yeast. We show that calcineurin lengthens arrest by prolonging Hog1-dependent activation of the poorly characterized cyclin-dependent kinase inhibitor Cip1. Cip1 only impacts cell cycle arrest in response to stressors that robustly activate calcineurin, suggesting that Cip1 is a context-specific regulator that differentially adjusts the length of arrest depending on the particular stressor.

Involvement of the High-Osmolarity Glycerol Pathway of Saccharomyces Cerevisiae in Protection against Copper Toxicity

Although essential for life, copper is also potentially toxic in concentrations that surpass physiological thresholds. The high-osmolarity glycerol pathway of yeast is the main regulator of adaptive responses and is known to play crucial roles in the responses to various stressors. The objective of this research is to determine whether the HOG pathway could be activated and to investigate the possible interplay of the HOG pathway and oxidative stress due to copper exposure. In this research, we demonstrate that copper could induce oxidative stress, including the elevated concentrations of reactive oxygen species (ROS) and malondialdehyde (MDA). Increased combination with GSH, increased intracellular SOD activity, and the up-regulation of relevant genes can help cells defend themselves against oxidative toxicity. The results show that copper treatment triggers marked and prolonged Hog1 phosphorylation. Significantly, oxidative stress generated by copper toxicity is essential for the activation of Hog1. Activated Hog1 is translocated to the nucleus to regulate the expressions of genes such as CTT1, GPD1, and HSP12, among others. Furthermore, copper exposure induced significant G1-phase cell cycle arrest, while Hog1 partially participated in the regulation of cell cycle progression. These novel findings reveal another role for Hog1 in the regulation of copper-induced cellular stress.

Induction of resistance mechanisms in Rhodotorula toruloides for growth in sugarcane hydrolysate with high inhibitor content

The oleaginous yeast Rhodotorula toruloides is a potential lipid producer for biodiesel production. However, this yeast shows growth inhibition due to harmful compounds when cultivated in hemicellulose hydrolysate. Here, we present a comparative analysis of colony selection and heterologous adaptive laboratory enhancement (ALE) strategies for obtaining robust strains. We implemented these ALE strategies for R. toruloides in a culture medium containing sugarcane hemicellulose hydrolysate. Our comparison study showed that the strain obtained with heterogeneous ALE strategy (Rth) reached a µ_max of 55% higher than the parental strain. It also exhibited higher biomass production (6.51 g/l) and lipid content (60%). ALE with colony selection strategy (Rtc) had a fitness gain in terms of shortening of the lag phase (9 h) when compared to Rth and parental strain (11.67, 12.33 h, respectively). When cultivated in Eucalyptus urograndis hemicellulose hydrolysate, the Rth strain achieved a high lipid content, 64%. Kinetics studies showed a strong effect of acetic acid as a repressor of xylose consumption during R. toruloides cultivation.Key points• Distinct adaptive laboratory strategies resulted in strains with different physiologies.• Heterologous adaptive laboratory enhancement provided the best results (fitness gain of 55% in µmax).• The Rth strain achieved a lipid content of 64.3% during cultivation in eucalyptus hemicellulose hydrolysate.

Attrition und Osmokinetik – Zwei Konzepte zur Pathogenese des Trockenen Auges

Die neuen Erkenntnisse der Pathophysiolgie des Trockenen Auges erkennen das Zusammenspiel von Tränen, Augenoberfläche und Lidoberfläche als eine funktionelle Einheit an. Der Begriff der Benetzungsfähigkeit der Tränen in Abhängigkeit der mikrotektonischen Anatomie der Augenoberfläche relativiert die Anforderungen an Träne und Tränenersatzmittel. Das Model der Attrition, welches die Effekte der friktionsneutralisierenden Kapazität des Tränenfilms, der Reibung und die Bedeutung der Mechanotransduktionskapazität des Epithels zusammenfasst, wird eingeführt und dessen pathophysiologische Bedeutung erläutert. Attrition und Benetzung bestimmen zusammen grundlegende pathophysiologische Vorgänge in der Augenoberfläche wie Aktivierung von Nerven (subjektive Beschwerden) sowie Entzündung und beeinflussen damit die Dynamik der Pathophysiologie, und den Übergang von vorübergehenden Beschwerden zu einer manifesten Erkrankung des Trockenen Auges. Die Betrachtung der Osmolarität als numerischer statischer Grenzwert zur alleinigen Diagnose des Trockenen Auges ist klinisch nicht haltbar. Das neue, dynamische Model der Osmokinetik, zeigt dagegen eine Alternative auf, in der die Tageschwankungen und die Beachtung des durchschnittlichen Osmolaritätsniveaus gröβere Bedeutung gewinnen und damit der eigentlichen pathophysiologischen Bedeutung der Osmolarität gerechter wird.