Yeast synthetic minimal biosensors for evaluating protein production

2020 ◽  
Author(s):  
Kai Peng ◽  
Heinrich Koukamp ◽  
Isak S. Pretorius ◽  
Ian T. Paulsen

AbstractThe unfolded protein response (UPR) is a highly conserved cellular response in eukaryotic cells to counteract endoplasmic reticulum (ER) stress, typically triggered by unfolded protein accumulation. In addition to its relevance to human diseases like cancer cell development, the induction of the UPR has a significant impact on recombinant protein production yields in microbial cell factories, including the industrial workhorse Saccharomyces cerevisiae. Being able to accurately detect and measure this ER stress response in single cells, enables the rapid optimisation of protein production conditions and high-throughput strain selection strategies. Current methodologies to monitor the UPR in S. cerevisiae are often temporally and spatially removed from the cultivation stage, or lack updated systematic evaluation. To this end we constructed and systematically evaluated a series of high-throughput UPR sensors by different designs, incorporating either yeast native UPR promoters or novel synthetic minimal UPR promoters. The native promoters of DER1 and ERO1 were identified to have suitable UPR biosensor properties and served as an expression level guide for orthogonal sensor benchmarking. Our best synthetic minimal sensor, SM1, was only 98 bp in length, had minimal homology to other native yeast sequences and displayed superior sensor characteristics. Using this synthetic minimal UPR sensor, we demonstrate its ability to accurately discriminate between cells expressing different heterologous proteins and at varying production levels. Our sensor is thus a novel high-throughput tool for determining expression/engineering strategies for optimal heterologous protein production.

2021 ◽  
Vol 12 ◽  
Author(s):  
Michael Panting ◽  
Inger Baeksted Holme ◽  
Jón Már Björnsson ◽  
Yingxin Zhong ◽  
Henrik Brinch-Pedersen

The use of plants as heterologous hosts to produce recombinant proteins has some intriguing advantages. There is, however, the potential of overloading the endoplasmic reticulum (ER) capacity when producing recombinant proteins in the seeds. This leads to an ER-stress condition and accumulating of unfolded proteins. The unfolded protein response (UPR) is activated to alleviate the ER-stress. With the aim to increase the yield of human epidermal growth factor (EGF) and mouse leukemia inhibitory factor (mLIF) in barley, we selected genes reported to have increased expression during ER-induced stress. The selected genes were calreticulin (CRT), protein disulfide isomerase (PDI), isopentenyl diphosphate isomerase (IPI), glutathione-s-transferase (GST), HSP70, HSP26, and HSP16.9. These were knocked out using CRISPR/Cas9 or overexpressed by conventional transgenesis. The generated homozygous barley lines were crossed with barley plants expressing EGF or mLIF and the offspring plants analyzed for EGF and mLIF protein accumulation in the mature grain. All manipulated genes had an impact on the expression of UPR genes when plantlets were subjected to tunicamycin (TN). The PDI knockout plant showed decreased protein body formation, with protein evenly distributed in the cells of the endosperm. The two genes, GST and IPI, were found to have a positive effect on recombinant protein production. mLIF expression was increased in a F2 homozygous GST knockout mutant background as compared to a F2 GST wild-type offspring. The overexpression of IPI in a F1 cross showed a significant increase in EGF expression. We demonstrate that manipulation of UPR related genes can have a positive effect on recombinant protein accumulation.


Life ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1376
Author(s):  
Mateusz Kowalczyk ◽  
Edward Kowalczyk ◽  
Paweł Kwiatkowski ◽  
Łukasz Łopusiewicz ◽  
Monika Talarowska ◽  
...  

Despite many scientific studies on depression, there is no clear conception explaining the causes and mechanisms of depression development. Research conducted in recent years has shown that there is a strong relationship between depression and the endoplasmic reticulum (ER) stress. In order to restore ER homeostasis, the adaptive unfolded protein response (UPR) mechanism is activated. Research suggests that ER stress response pathways are continuously activated in patients with major depressive disorders (MDD). Therefore, it seems that the recommended drugs should reduce ER stress. A search is currently underway for drugs that will be both effective in reducing ER stress and relieving symptoms of depression.


PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0258005
Author(s):  
Worarat Kruasuwan ◽  
Aekkachai Puseenam ◽  
Chitwadee Phithakrotchanakoon ◽  
Sutipa Tanapongpipat ◽  
Niran Roongsawang

The thermotolerant methylotrophic yeast Ogataea thermomethanolica TBRC 656 is a potential host strain for industrial protein production. Heterologous proteins are often retained intracellularly in yeast resulting in endoplasmic reticulum (ER) stress and poor secretion, and despite efforts to engineer protein secretory pathways, heterologous protein production is often lower than expected. We hypothesized that activation of genes involved in the secretory pathway could mitigate ER stress. In this study, we created mutants defective in protein secretory-related functions using clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated protein 9 (Cas9) tools. Secretion of the model protein xylanase was significantly decreased in loss of function mutants for oxidative stress (sod1Δ) and vacuolar and protein sorting (vps1Δ and ypt7Δ) genes. However, xylanase secretion was unaffected in an autophagy related atg12Δ mutant. Then, we developed a system for sequence-specific activation of target gene expression (CRISPRa) in O. thermomethanolica and used it to activate SOD1, VPS1 and YPT7 genes. Production of both non-glycosylated xylanase and glycosylated phytase was enhanced in the gene activated mutants, demonstrating that CRISPR-Cas9 systems can be used as tools for understanding O. thermomethanolica genes involved in protein secretion, which could be applied for increasing heterologous protein secretion in this yeast.


2021 ◽  
Author(s):  
◽  
Peter William Bircham

<p>Proteins traversing the secretory pathway begin their passage in the endoplasmic reticulum (ER) where they must be correctly folded and processed to pass quality control measures. Complications with this process can result in the accumulation of misfolded proteins, commonly referred to as ER-stress, which has been associated with a number of diseases. The unfolded protein response (UPR) is the cell’s mechanism of dealing with ER-stress and is activated via the IRE1-HAC1 pathway in yeast. Ire1p is the ER-stress sensor and upon recognising misfolded proteins Ire1 oligomerises and forms local clusters. Activated Ire1p then splices out an inhibitory intron from the UPR specific transcription factor Hac1p which goes on to initiate downstream responses to alleviate ER-stress. Here we utilise high-throughput microscopy and UPR-specific GFP reporter systems to characterise the UPR in the yeast Saccharomyces cerevisiae. High-throughput microscopy and automated image analysis is increasingly being used as a screening tool for investigating genome-wide collections of yeast strains, including the yeast deletion mutant array and the yeast GFP collection. We describe the use of GFP labelled Ire1p to visualise cluster formation as a reporter for early UPR recognition of misfolded proteins, as well as a GFP controlled by a Hac1p responsive promoter to measure downstream UPR activation. These UPR-specific GFP reporter systems were used to screen a collection of non-essential gene deletion strains, identifying gene deletions that induce UPR activation and thus are likely to function in the early secretory pathway. This included well known components such as the ALG members of the glycosylation pathway and various ER chaperones such as LHS1 and SCJ1. Additionally this analysis revealed 44 previously uncharacterised genes, suggesting there are still processes related to the secretory pathway that are yet to be described. Moreover, by inducing ER-stress in this screening system we revealed genes required for the normal activation of the UPR including ribosomal/translation and chromatin/transcriptionally related genes, as well as various genes from throughout the secretory pathway. Furthermore, we screened a collection of ~4000 strains, each expressing a different GFP fusion protein, under ER-stress conditions to identify protein expression and localisation changes induced by the UPR. Comparison to UPR deficient Δhac1 cells uncovered a set of UPR specific targets including 26 novel UPR targets that had not been identified in previous studies measuring changes at the transcript level. As part of this work, we developed a dual red fluorescent protein system to label cells for automated image segmentation to enable single cell phenotype measurements. Here we describe the use of texture analysis as a means of increasing automation in the identification of phenotypic changes across the proteome. These novel techniques may be more widely applied to screening GFP collections to increase automation of image analysis, particularly as manual annotation of phenotypic changes is a major bottleneck in high-throughput screening. The results presented here from microscopy based screening compare well with other techniques in the literature, but also provide new information highlighting the synergistic effects of integrating high-throughput imaging into traditional screening methodologies.</p>


2018 ◽  
Vol 29 (25) ◽  
pp. 3052-3062 ◽  
Author(s):  
Wylie Stroberg ◽  
Hadar Aktin ◽  
Yonatan Savir ◽  
Santiago Schnell

Cellular protein homeostasis requires continuous monitoring of stress in the endoplasmic reticulum (ER). Stress-detection networks control protein homeostasis by mitigating the deleterious effects of protein accumulation, such as aggregation and misfolding, with precise modulation of chaperone production. Here, we develop a coarse model of the unfolded protein response in yeast and use multi-objective optimization to determine which sensing and activation strategies optimally balance the trade-off between unfolded protein accumulation and chaperone production. By comparing a stress-sensing mechanism that responds directly to the level of unfolded protein in the ER to a mechanism that is negatively regulated by unbound chaperones, we show that chaperone-mediated sensors are more efficient than sensors that detect unfolded proteins directly. This results from the chaperone-mediated sensor having separate thresholds for activation and deactivation. Finally, we demonstrate that a sensor responsive to both unfolded protein and unbound chaperone does not further optimize homeostatic control. Our results suggest a strategy for designing stress sensors and may explain why BiP-mitigated ER stress-sensing networks have evolved.


Author(s):  
Divya Saro Varghese ◽  
Bassam R. Ali

The oxidative modification of the major cholesterol carrying lipoprotein, oxLDL, is a biomarker as well as a pathological factor in cardiovascular diseases (CVD), type 2 diabetes mellitus (T2DM), obesity and other metabolic diseases. Perturbed cellular homeostasis due to physiological, pathological and pharmacological factors hinder the proper functioning of the endoplasmic reticulum (ER), which is the major hub for protein folding and processing, lipid biosynthesis and calcium storage, thereby leading to ER stress. The cellular response to ER stress is marked by a defensive mechanism called unfolded protein response (UPR), wherein the cell adapts strategies that favor survival. Under conditions of excessive ER stress, when the survival mechanisms fail to restore balance, UPR switches to apoptosis and eliminates the defective cells. ER stress is a major hallmark in metabolic syndromes such as diabetes, non-alcoholic fatty liver disease (NAFLD), neurological and cardiovascular diseases. Though the pathological link between oxLDL and ER stress in cardiovascular diseases is well-documented, its involvement in other diseases is still largely unexplored. This review provides a deep insight into the common mechanisms in the pathogenicity of diseases involving oxLDL and ER stress as key players. In addition, the potential therapeutic intervention of the targets implicated in the pathogenic processes are also explored.


2021 ◽  
Author(s):  
◽  
Peter William Bircham

<p>Proteins traversing the secretory pathway begin their passage in the endoplasmic reticulum (ER) where they must be correctly folded and processed to pass quality control measures. Complications with this process can result in the accumulation of misfolded proteins, commonly referred to as ER-stress, which has been associated with a number of diseases. The unfolded protein response (UPR) is the cell’s mechanism of dealing with ER-stress and is activated via the IRE1-HAC1 pathway in yeast. Ire1p is the ER-stress sensor and upon recognising misfolded proteins Ire1 oligomerises and forms local clusters. Activated Ire1p then splices out an inhibitory intron from the UPR specific transcription factor Hac1p which goes on to initiate downstream responses to alleviate ER-stress. Here we utilise high-throughput microscopy and UPR-specific GFP reporter systems to characterise the UPR in the yeast Saccharomyces cerevisiae. High-throughput microscopy and automated image analysis is increasingly being used as a screening tool for investigating genome-wide collections of yeast strains, including the yeast deletion mutant array and the yeast GFP collection. We describe the use of GFP labelled Ire1p to visualise cluster formation as a reporter for early UPR recognition of misfolded proteins, as well as a GFP controlled by a Hac1p responsive promoter to measure downstream UPR activation. These UPR-specific GFP reporter systems were used to screen a collection of non-essential gene deletion strains, identifying gene deletions that induce UPR activation and thus are likely to function in the early secretory pathway. This included well known components such as the ALG members of the glycosylation pathway and various ER chaperones such as LHS1 and SCJ1. Additionally this analysis revealed 44 previously uncharacterised genes, suggesting there are still processes related to the secretory pathway that are yet to be described. Moreover, by inducing ER-stress in this screening system we revealed genes required for the normal activation of the UPR including ribosomal/translation and chromatin/transcriptionally related genes, as well as various genes from throughout the secretory pathway. Furthermore, we screened a collection of ~4000 strains, each expressing a different GFP fusion protein, under ER-stress conditions to identify protein expression and localisation changes induced by the UPR. Comparison to UPR deficient Δhac1 cells uncovered a set of UPR specific targets including 26 novel UPR targets that had not been identified in previous studies measuring changes at the transcript level. As part of this work, we developed a dual red fluorescent protein system to label cells for automated image segmentation to enable single cell phenotype measurements. Here we describe the use of texture analysis as a means of increasing automation in the identification of phenotypic changes across the proteome. These novel techniques may be more widely applied to screening GFP collections to increase automation of image analysis, particularly as manual annotation of phenotypic changes is a major bottleneck in high-throughput screening. The results presented here from microscopy based screening compare well with other techniques in the literature, but also provide new information highlighting the synergistic effects of integrating high-throughput imaging into traditional screening methodologies.</p>


Author(s):  
Jonathan Turpin ◽  
Etienne Frumence ◽  
Wissal Harrabi ◽  
Chaker El Kalamouni ◽  
Philippe Desprès ◽  
...  

Flaviviruses replicate in membranous factories associated with the endoplasmic reticulum (ER). The replication rate generates a high polyprotein integration that can contribute to ER stress. Therefore, the host cell can develop an Unfolded Protein Response (UPR) to this protein accumulation which will stimulate appropriate cellular responses in the infectious context (Adaptation, autophagy or cell death). These different stress responses can help to overcome the virus and usually support antiviral strategies initiated by infected cells. In the present study, we investigated the capacity of ZIKA virus (ZIKV) to induce ER stress in epithelial A549 cells with a special focus on the causal factors behind it. We observed that the cells respond to ZIKV infection by implementing an UPR through activation of the IRE1 and PERK pathway but surprisingly without activation of the ATF6 branch. When we examined the effects of modulating the ER stress response we found that UPR inducers significantly inhibit ZIKV replication. Interestingly, our findings provide evidence that ZIKV can altered the UPR in order to escape to the host cell defense system.


Author(s):  
Tarah Satterfield ◽  
Jessica Pritchett ◽  
Sarah Cruz ◽  
Kyeorda Kemp

AbstractBackground: Transmissible spongiform encephalopathies are a collection of rare neurodegenerative disorders characterized by loss of neuronal cells, astrocytosis, and plaque formation. The causative agent of these diseases is thought to be abnormally folded prions and is characterized by a conformational change from normal, cellular prion protein (PrPc) to the abnormal form (PrPTSE). Although, there is evidence that normal prion protein can contribute to these disorders. The unfolded protein response, a conserved series of pathways involved in resolving stress associated with unfolded protein accumulation in the Endoplasmic Reticulum (ER), has been shown to play a role in regulating the development of prion diseases. Methods: This review chose papers based on their relevance to current studies involved in prion protein synthesis and transformation, identifies various links between prion diseases and ER stress, and reports on current and potential treatments as they relate to ER stress and prion diseases. Conclusion: For the advancement of prion disease treatment, it is important to understand the mechanisms involved in prion formation, and ER stress is implicated in prion disease progression. Therefore, targeting the ER or pathways involved in response to stress in the ER may help us treat prion diseases.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 986-986
Author(s):  
Chungyee Leung-Hagesteijn ◽  
Brad Wouters ◽  
Rodger E. Tiedemann

Abstract Abstract 986 We have previously conducted kinome- (Tiedemann et al., Blood 2010) and genome- (Zhu et al., Blood 2011) wide small interfering RNA (siRNA) studies in human myeloma cells in the absence and presence of titrated bortezomib (BTZ) in order to identify genes that modulate BTZ sensitivity or resistance. From high throughput RNAi screening, endoplasmic reticulum-to-nucleus-signaling-1 (ERN1), the human homolog of yeast IRE-1, was identified with multiple siRNA as the kinase most potently required for BTZ activity, with genetic silencing associated with BTZ resistance. ERN1/IRE1 is an endoplasmic reticulum (ER)-resident transmembrane protein and a core component of the unfolded protein response (UPR). By gene expression profiling and western blot IRE1 is ubiquitously expressed across primary myeloma tumors and a panel of 14 human myeloma tumor lines (HMCL). Significantly, silencing of IRE1 with lentiviral shRNA induced BTZ resistance in 9/9 HMCL. IRE1 silencing in the absence of BTZ was surprisingly well tolerated in the majority of HMCL tested, with no loss of viability; however in 2/9 HMCL (JJN3, 8226) silencing of IRE1 resulted in reduced proliferation. Multiple RNAi yielded identical results. In response to unfolded protein accumulation within the ER lumen, IRE1 oligomerizes and auto-phosphorylates to reveal an endonuclease activity that splices X-box protein 1 (XBP1) mRNA to activate the potent bZIP transcription factor, XBP1s. XBP1 is essential for physiologic differentiation of B cells to plasma cells and its absence results in profound plasma cell deficiency (Reimold et al., 2001). Despite it's essential role in plasma cell differentiation, we find that XBP1, like IRE1, is redundant for myeloma cell survival under standard growth conditions. Lentiviral knockdown of XBP1 using multiple distinct RNAi failed to induce HMCL cytotoxicity; and resulted in reduced growth in only 2/9 HMCL, closely mirroring results observed with IRE1 inhibition. Significantly, XBP1 silencing also closely reproduced the BTZ resistance observed with IRE1 silencing. As plasmacytoma in patients grow under hypoxic conditions we next evaluated myeloma cell growth in response to hypoxia (0.2% O2) and concurrent UPR signaling disruption. At 48hrs, viability was comparable in IRE1 knockouts and parental cells. In contrast, HMCL with IRE1 silencing showed marked vulnerability to protein synthesis inhibition induced by puromycin, with selection against IRE1 silenced cells in mixed cultures. Notably, ER stress is signaled by 3 different transmembrane transducers (IRE1, PERK and ATF6), each contributing to distinct UPR pathways. As induced BTZ resistance from IRE1 or XBP1 inhibition might conceivably result either from loss of a death signal transmitted via IRE1-XBP1 following PI-induced ER stress, or from a compensatory increase in PERK or ATF6 homeostasis signaling in response to IRE1-XBP1 silencing, we generated single, double and triple knockdown HMCL with suppressed expression of 1, 2 or all 3 ER stress transducers (IRE1, PERK, ATF6). Individual silencing of either IRE1 or PERK in HMCL had no effect on levels of other ER stress transducers by western blot, however silencing of ATF6 caused compensatory increases in PERK while XBP1 silencing resulted in reduced IRE1. Importantly, HMCL lacking IRE1 and PERK or ATF6, showed no loss of BTZ resistance induced by either IRE1 or XBP1 knockdown, demonstrating that secondary increases in signaling via these alternative ER stress pathways do not account for the BTZ resistance induced by IRE1-XBP1 pathway inhibition. Consistent with the hypothesis that increased UPR signaling (via IRE1-XBP1) causes myeloma cell death, knock down of the ER luminal chaperone BiP (HSPA5), which negatively regulates all 3 stress transducers, proved cytotoxic in multiple HMCL. Overall, these data suggest that the anti-myeloma activity of BTZ involves a specific IRE1-XBP1 death signal generated in response to proteasome inhibition and unfolded protein ER stress, rather than ER failure from unfolded protein. As IRE1-XBP1 signaling is dispensable for myeloma cell survival under many growth conditions, targeted small molecule inhibitors of IRE1 currently under development may prove ineffective as single agent therapy for myeloma; moreover such agents may prove antagonist to PI therapy. Finally, disruption of the IRE1-XBP1 axis in primary tumors may mediate bortezomib resistance in patients. Disclosures: No relevant conflicts of interest to declare.


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