scholarly journals Uncovering CAZyme Induction in the Thermophilic Fungus Thermoascus Aurantiacus

2021 ◽  
Author(s):  
Raphael Gabriel ◽  
Rebecca Mueller ◽  
Lena Floerl ◽  
Cynthia Hopson ◽  
Simon Harth ◽  
...  
Keyword(s):  
Plant Biomass ◽  
Thermophilic Fungus ◽  
Thermoascus Aurantiacus ◽  
Rna Seq ◽  
Thermostable Enzymes ◽  
Unfolded Protein ◽  
Highly Active ◽  
Biochemical Assays ◽  
Genome Wide ◽  
Protein Response

Abstract Background: Filamentous fungi are excellent lignocellulose degraders, which they achieve through producing carbohydrate active enzymes (CAZymes). CAZyme production is highly orchestrated and the application of –omics methods such as RNA-Seq has greatly expanded understanding of this important biotechnological process. The thermophilic fungus Thermoascus aurantiacus secretes high amounts of highly active thermostable enzymes that enable saccharifications at higher temperatures; however, the genome-wide response to CAZyme induction is not understood. Results: A fed-batch system with plant biomass-derived sugars D-xylose, L-arabinose and cellobiose established that these sugars induce CAZyme expression in T. aurantiacus. The C5 sugars induced both cellulases and hemicellulases, while cellobiose specifically induced cellulases. A minimal medium formulation was developed to enable RNA-seq studies of T. aurantiacus with these inducers. It was found that D-xylose and L-arabinose strongly induced a wide variety of CAZymes, auxiliary activity (AA) enzymes and carbohydrate esterases (CEs), while cellobiose facilitated lower expression of mostly cellulase genes. Furthermore, putative orthologues of different unfolded protein response genes were up-regulated during the C5 sugar feeding together with genes in the C5 sugar assimilation pathways. Conclusion: This work has identified two additional CAZyme inducers for T. aurantiacus, L-arabinose and cellobiose, along with D-xylose. A combination of biochemical assays and RNA-seq measurements established that C5 sugars induce a suite of cellulases and hemicellulases, providing a path to produce a broad spectrum thermotolerant enzymatic mixture for deconstruction of plant biomass.

scholarly journals CAZymes from the thermophilic fungus Thermoascus aurantiacus are induced by C5 and C6 sugars

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Raphael Gabriel ◽  
Rebecca Mueller ◽  
Lena Floerl ◽  
Cynthia Hopson ◽  
Simon Harth ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plant Biomass ◽  
Thermophilic Fungus ◽  
Thermoascus Aurantiacus ◽  
Thermostable Enzymes ◽  
Unfolded Protein ◽  
Highly Active ◽  
Biochemical Assays ◽  
Gene Expression Studies ◽  
Protein Response

Abstract Background Filamentous fungi are excellent lignocellulose degraders, which they achieve through producing carbohydrate active enzymes (CAZymes). CAZyme production is highly orchestrated and gene expression analysis has greatly expanded understanding of this important biotechnological process. The thermophilic fungus Thermoascus aurantiacus secretes highly active thermostable enzymes that enable saccharifications at higher temperatures; however, the genome-wide measurements of gene expression in response to CAZyme induction are not understood. Results A fed-batch system with plant biomass-derived sugars d-xylose, l-arabinose and cellobiose established that these sugars induce CAZyme expression in T. aurantiacus. The C5 sugars induced both cellulases and hemicellulases, while cellobiose specifically induced cellulases. A minimal medium formulation was developed to enable gene expression studies of T. aurantiacus with these inducers. It was found that d-xylose and l-arabinose strongly induced a wide variety of CAZymes, auxiliary activity (AA) enzymes and carbohydrate esterases (CEs), while cellobiose facilitated lower expression of mostly cellulase genes. Furthermore, putative orthologues of different unfolded protein response genes were up-regulated during the C5 sugar feeding together with genes in the C5 sugar assimilation pathways. Conclusion This work has identified two additional CAZyme inducers for T. aurantiacus, l-arabinose and cellobiose, along with d-xylose. A combination of biochemical assays and RNA-seq measurements established that C5 sugars induce a suite of cellulases and hemicellulases, providing paths to produce broad spectrum thermotolerant enzymatic mixtures.

The genetics of axial spondyloarthritis

2016 ◽  
Author(s):  
Stefan Siebert ◽  
Sengupta Raj ◽  
Alexander Tsoukas
Keyword(s):  
Axial Spondyloarthritis ◽  
Association Studies ◽  
Single Gene ◽  
Twin Studies ◽  
Genome Wide Association Studies ◽  
Functional Importance ◽  
Unfolded Protein ◽  
Genome Wide ◽  
Arthritogenic Peptide ◽  
Protein Response

Family and twin studies have long suggested a large genetic component in ankylosing spondylitis (AS). The genetic association with HLA-B27 remains one of the strongest single gene variant associations reported in any complex polygenic disease. The exact mechanism by which HLA-B27 contributes to AS remains unknown, with three main theories proposed: the arthritogenic peptide, endoplasmic reticulum stress with unfolded protein response, and homodimerization theories. Genome-wide association studies have identified a number of other important susceptibility genes for AS, several of which overlap with other spondyloarthritis conditions. Of these, ERAP1 and IL-23R, are covered in more detail, highlighting their functional importance.

scholarly journals Venezuelan Equine Encephalitis Virus Induces Apoptosis through the Unfolded Protein Response Activation of EGR1

2016 ◽  
Vol 90 (7) ◽  
pp. 3558-3572 ◽  
Author(s):  
Alan Baer ◽  
Lindsay Lundberg ◽  
Danielle Swales ◽  
Nicole Waybright ◽  
Chelsea Pinkham ◽  
...  
Keyword(s):  
Unfolded Protein Response ◽  
Venezuelan Equine Encephalitis Virus ◽  
Encephalitis Virus ◽  
Rna Seq ◽  
Venezuelan Equine Encephalitis ◽  
Equine Encephalitis Virus ◽  
Unfolded Protein ◽  
The Unfolded Protein Response ◽  
Protein Response ◽  
Early Growth Response 1

ABSTRACTVenezuelan equine encephalitis virus (VEEV) is a previously weaponized arthropod-borne virus responsible for causing acute and fatal encephalitis in animal and human hosts. The increased circulation and spread in the Americas of VEEV and other encephalitic arboviruses, such as eastern equine encephalitis virus and West Nile virus, underscore the need for research aimed at characterizing the pathogenesis of viral encephalomyelitis for the development of novel medical countermeasures. The host-pathogen dynamics of VEEV Trinidad donkey-infected human astrocytoma U87MG cells were determined by carrying out RNA sequencing (RNA-Seq) of poly(A) and mRNAs. To identify the critical alterations that take place in the host transcriptome following VEEV infection, samples were collected at 4, 8, and 16 h postinfection and RNA-Seq data were acquired using an Ion Torrent PGM platform. Differential expression of interferon response, stress response factors, and components of the unfolded protein response (UPR) was observed. The protein kinase RNA-like endoplasmic reticulum kinase (PERK) arm of the UPR was activated, as the expression of both activating transcription factor 4 (ATF4) and CHOP (DDIT3), critical regulators of the pathway, was altered after infection. Expression of the transcription factor early growth response 1 (EGR1) was induced in a PERK-dependent manner. EGR1−/−mouse embryonic fibroblasts (MEFs) demonstrated lower susceptibility to VEEV-induced cell death than isogenic wild-type MEFs, indicating that EGR1 modulates proapoptotic pathways following VEEV infection. The influence of EGR1 is of great importance, as neuronal damage can lead to long-term sequelae in individuals who have survived VEEV infection.IMPORTANCEAlphaviruses represent a group of clinically relevant viruses transmitted by mosquitoes to humans. In severe cases, viral spread targets neuronal tissue, resulting in significant and life-threatening inflammation dependent on a combination of virus-host interactions. Currently there are no therapeutics for infections cause by encephalitic alphaviruses due to an incomplete understanding of their molecular pathogenesis. Venezuelan equine encephalitis virus (VEEV) is an alphavirus that is prevalent in the Americas and that is capable of infecting horses and humans. Here we utilized next-generation RNA sequencing to identify differential alterations in VEEV-infected astrocytes. Our results indicated that the abundance of transcripts associated with the interferon and the unfolded protein response pathways was altered following infection and demonstrated that early growth response 1 (EGR1) contributed to VEEV-induced cell death.

scholarly journals Cu, Zn Superoxide Dismutase and NADP(H) Homeostasis Are Required for Tolerance of Endoplasmic Reticulum Stress inSaccharomyces cerevisiae

2009 ◽  
Vol 20 (5) ◽  
pp. 1493-1508 ◽  
Author(s):  
Shi-Xiong Tan ◽  
Mariati Teo ◽  
Yuen T. Lam ◽  
Ian W. Dawes ◽  
Gabriel G. Perrone
Keyword(s):  
Endoplasmic Reticulum ◽  
Superoxide Dismutase ◽  
Er Stress ◽  
Stress Sensitivity ◽  
Pentose Phosphate ◽  
Unfolded Protein ◽  
Genome Wide ◽  
The Unfolded Protein Response ◽  
Protein Response

Genome-wide screening for sensitivity to chronic endoplasmic reticulum (ER) stress induced by dithiothreitol and tunicamycin (TM) identified mutants deleted for Cu, Zn superoxide dismutase (SOD) function (SOD1, CCS1) or affected in NADPH generation via the pentose phosphate pathway (TKL1, RPE1). TM-induced ER stress led to an increase in cellular superoxide accumulation and an increase in SOD1 expression and Sod1p activity. Prior adaptation of the hac1 mutant deficient in the unfolded protein response (UPR) to the superoxide-generating agent paraquat reduced cell death under ER stress. Overexpression of the ER oxidoreductase Ero1p known to generate hydrogen peroxide in vitro, did not lead to increased superoxide levels in cells subjected to ER stress. The mutants lacking SOD1, TKL1, or RPE1 exhibited decreased UPR induction under ER stress. Sensitivity of the sod1 mutant to ER stress and decreased UPR induction was partially rescued by overexpression of TKL1 encoding transketolase. These data indicate an important role for SOD and cellular NADP(H) in cell survival during ER stress, and it is proposed that accumulation of superoxide affects NADP(H) homeostasis, leading to reduced UPR induction during ER stress.

scholarly journals Deciphering the Regulatory Network between the SREBP Pathway and Protein Secretion in Neurospora crassa

mBio ◽  
2017 ◽  
Vol 8 (2) ◽  
Author(s):  
Lina Qin ◽  
Vincent W. Wu ◽  
N. Louise Glass
Keyword(s):  
Neurospora Crassa ◽  
Unfolded Protein Response ◽  
Molecular Oxygen ◽  
Protein Secretion ◽  
Plant Biomass ◽  
Unfolded Protein ◽  
Lytic Polysaccharide Monooxygenases ◽  
Polysaccharide Monooxygenases ◽  
The Unfolded Protein Response ◽  
Protein Response

ABSTRACT Sterol regulatory element binding proteins (SREBPs) are conserved from yeast to mammalian cells and function in the regulation of sterol homeostasis. In fungi, the SREBP pathway has been implicated in the adaptation to hypoxia and in virulence. In Neurospora crassa and Trichoderma reesei, the SREBP pathway also negatively regulates protein secretion under lignocellulolytic conditions. Here we utilized global transcriptional profiling combined with genetic and physiological analyses to address the regulatory link between the SREBP pathway and protein secretion in N. crassa. Our results demonstrated that the function of the SREBP pathway in ergosterol biosynthesis and adaptation to hypoxia was conserved in N. crassa. Under lignocellulolytic conditions, the SREBP pathway was highly activated, resulting in the reduced expression of lytic polysaccharide monooxygenases, which require molecular oxygen for catalytic activity. Additionally, activation of the SREBP pathway under lignocellulolytic conditions repressed a set of genes predicted to be involved in the endoplasmic reticulum stress response. Here we show that the inability of a hac-1 mutant, which bears a deletion of the major regulator of the unfolded protein response (UPR), to efficiently produce cellulases and utilize cellulose was suppressed by mutations in the SREBP pathway. The analyses presented here demonstrated new SREBP pathway functions, including linkages to the UPR, and provide new clues for genetic engineering of filamentous fungi to improve their production of extracellular proteins. IMPORTANCE The role of SREBP transcription factors in the regulation of sterol biosynthesis is conserved from humans to yeast. In filamentous fungi, this pathway regulates the secretion of lignocellulolytic enzymes during plant biomass deconstruction. Here we show that the SREBP pathway in Neurospora crassa regulates the production of specific cellulases, lytic polysaccharide monooxygenases that utilize molecular oxygen. Via global transcriptional profile and genetic analyses, a relationship between the SREBP pathway and the unfolded protein response (UPR) pathway was revealed, suggesting a regulatory interplay of these two pathways in the trafficking of plant biomass-degrading enzymes. These findings have implications for our understanding of the cross talk of the SREBP and UPR pathways in other organisms and will guide the rational engineering of fungal strains to improve cellulolytic enzyme production. IMPORTANCE The role of SREBP transcription factors in the regulation of sterol biosynthesis is conserved from humans to yeast. In filamentous fungi, this pathway regulates the secretion of lignocellulolytic enzymes during plant biomass deconstruction. Here we show that the SREBP pathway in Neurospora crassa regulates the production of specific cellulases, lytic polysaccharide monooxygenases that utilize molecular oxygen. Via global transcriptional profile and genetic analyses, a relationship between the SREBP pathway and the unfolded protein response (UPR) pathway was revealed, suggesting a regulatory interplay of these two pathways in the trafficking of plant biomass-degrading enzymes. These findings have implications for our understanding of the cross talk of the SREBP and UPR pathways in other organisms and will guide the rational engineering of fungal strains to improve cellulolytic enzyme production.

scholarly journals Genome-wide analysis reveals a switch in the translational program upon oocyte meiotic resumption

2019 ◽  
Author(s):  
Xuan G. Luong ◽  
Enrico Maria Daldello ◽  
Gabriel Rajkovic ◽  
Cai-Rong Yang ◽  
Marco Conti
Keyword(s):  
Mrna Translation ◽  
Messenger Rnas ◽  
Rna Seq ◽  
Genome Wide Analysis ◽  
Meiotic Progression ◽  
Maternal Mrna ◽  
Highly Active ◽  
Genome Wide ◽  
Molecular Machinery ◽  
Maternal Mrnas

SummaryDuring oocyte maturation, changes in gene expression depend exclusively on translation and degradation of maternal mRNAs rather than transcription. Execution of this translation program is essential for assembling the molecular machinery required for meiotic progression, fertilization, and embryo development. With the present study, we used a RiboTag/RNA-Seq approach to explore the timing of maternal mRNA translation in quiescent oocytes as well as in oocytes progressing through the first meiotic division. This genome-wide analysis reveals a global switch in maternal mRNA translation coinciding with oocyte re-entry into the meiotic cell cycle. Messenger RNAs whose translation is highly active in quiescent oocytes invariably become repressed during meiotic re-entry, whereas transcripts repressed in quiescent oocytes become activated. Experimentally, we have defined the exact timing of the switch, the repressive function of CPE elements, and identified a novel role for CPEB1 in maintaining constitutive translation of a large group of maternal mRNAs during maturation.

scholarly journals Protomer alignment modulates specificity of RNA substrate recognition by Ire1

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Weihan Li ◽  
Kelly Crotty ◽  
Diego Garrido Ruiz ◽  
Mark Voorhies ◽  
Carlos Rivera ◽  
...  
Keyword(s):  
Substrate Recognition ◽  
Mrna Splicing ◽  
Functional Specialization ◽  
Salt Bridges ◽  
Site Specific ◽  
Dimer Interface ◽  
Unfolded Protein ◽  
Biochemical Assays ◽  
The Unfolded Protein Response ◽  
Protein Response

The unfolded protein response (UPR) maintains protein folding homeostasis in the endoplasmic reticulum (ER). In metazoan cells, the Ire1 branch of the UPR initiates two functional outputs—non-conventional mRNA splicing and selective mRNA decay (RIDD). By contrast, Ire1 orthologs from Saccharomyces cerevisiae and Schizosaccharomyces pombe are specialized for only splicing or RIDD, respectively. Previously, we showed that the functional specialization lies in Ire1's RNase activity, which is either stringently splice-site specific or promiscuous (W. Li et al., 2018). Here, we developed an assay that reports on Ire1's RNase promiscuity. We found that conversion of two amino acids within the RNase domain of S. cerevisiae Ire1 to their S. pombe counterparts rendered it promiscuous. Using biochemical assays and computational modeling, we show that the mutations rewired a pair of salt bridges at Ire1 RNase domain's dimer interface, changing its protomer alignment. Thus, Ire1 protomer alignment affects its substrates specificity.

scholarly journals Genome-wide analysis reveals a switch in the translational program upon oocyte meiotic resumption

2020 ◽  
Vol 48 (6) ◽  
pp. 3257-3276 ◽  
Author(s):  
Xuan G Luong ◽  
Enrico Maria Daldello ◽  
Gabriel Rajkovic ◽  
Cai-Rong Yang ◽  
Marco Conti
Keyword(s):  
Mrna Translation ◽  
Messenger Rnas ◽  
Rna Seq ◽  
Genome Wide Analysis ◽  
Meiotic Progression ◽  
Maternal Mrna ◽  
Highly Active ◽  
Genome Wide ◽  
Molecular Machinery ◽  
Maternal Mrnas

Abstract During oocyte maturation, changes in gene expression depend exclusively on translation and degradation of maternal mRNAs rather than transcription. Execution of this translation program is essential for assembling the molecular machinery required for meiotic progression, fertilization, and embryo development. With the present study, we used a RiboTag/RNA-Seq approach to explore the timing of maternal mRNA translation in quiescent oocytes as well as in oocytes progressing through the first meiotic division. This genome-wide analysis reveals a global switch in maternal mRNA translation coinciding with oocyte re-entry into the meiotic cell cycle. Messenger RNAs whose translation is highly active in quiescent oocytes invariably become repressed during meiotic re-entry, whereas transcripts repressed in quiescent oocytes become activated. Experimentally, we have defined the exact timing of the switch and the repressive function of CPE elements, and identified a novel role for CPEB1 in maintaining constitutive translation of a large group of maternal mRNAs during maturation.

scholarly journals Regulation of the unfolded protein response transducer IRE1α by SERPINH1 aggravates periodontitis with diabetes mellitus via prolonged ER stress

2021 ◽  
Author(s):  
Mengdi Li ◽  
Shuheng Huang ◽  
Yong Zhang ◽  
Zhi Song ◽  
Haijun Fu ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Er Stress ◽  
Signaling Pathway ◽  
Rna Seq ◽  
Unfolded Protein ◽  
Periodontal Inflammation ◽  
Gingival Epithelium ◽  
The Unfolded Protein Response ◽  
Protein Response

Abstract Background The hyperglycemic microenvironment induced by diabetes mellitus aggravates the inflammatory response, in which the inositol-requiring enzyme-1α (IRE1α) signal transduction pathway of the unfolded protein response (UPR) participates. This study aimed to investigate the mechanism by which hyperglycemia regulates the IRE1α signaling pathway and affects endoplasmic reticulum (ER) homeostasis in human gingival epithelium in periodontitis with diabetes mellitus (DP). Methods Human gingival epithelium samples from healthy subjects, subjects with periodontitis and subjects with DP were collected, in vitro cultures of human gingival epithelial cells were challenged with a hyperglycemic microenvironment to observe the effects of diabetes on periodontal inflammation and to assess UPR-IRE1α signaling in human gingival epithelium in DP. Subsequently, RNA sequencing (RNA-seq) data was analyzed to investigate the expression of ER-related genes in human gingival epithelium. Furthermore, to explore the key role of serpin family H member 1 (SERPINH1) in the regulation of UPR-IRE1α signaling in a hyperglycemic microenvironment, experiments in SERPINH1-knockdown and SERPINH1-overexpression models were established in vitro. Results Diabetes causes a hyperinflammatory response in human gingival epithelium, which accelerates periodontal inflammation. A hyperglycemic microenvironment inhibited the inositol-requiring enzyme-1α / X-box binding protein 1 (IRE1α/XBP1) axis, decreased the expression of glucose regulated protein 78 (GRP78), and ultimately impaired the UPR, causing ER stress to be prolonged or more severe in human gingival epithelium. The RNA-seq and experiments revealed that the mechanism by which periodontitis is aggravated in individuals with diabetes mellitus may involve decreased SERPINH1 expression. SERPINH1 might act as an activator of IRE1α, maintaining human gingival epithelium homeostasis, suppressing nuclear factor-κB signaling pathway and reducing NOD-like receptor, pyrin domain containing protein 3 (NLRP3) and interleukin-1 beta (IL-1β) expression by preventing prolonged ER stress induced by high-glucose conditions. Conclusion Regulation of the UPR transducer IRE1α by SERPINH1 alleviates DP by mitigating prolonged ER stress.

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