scholarly journals Evolution of the folding landscape of effector caspases

2021 ◽  
Author(s):  
Suman Shrestha ◽  
Allan Clay Clark
Keyword(s):  
Common Ancestor ◽  
Enzyme Stability ◽  
Protein Structures ◽  
Fine Tuning ◽  
Dependent Manner ◽  
Effector Caspases ◽  
Initiator Caspases ◽  
Activation Mechanisms ◽  
Caspase Family ◽  
Oligomeric Forms

Caspases are a family of cysteinyl proteases that control programmed cell death and maintain homeostasis in multicellular organisms. The caspase family is an excellent model to study protein evolution because all caspases are produced as zymogens (procaspases) that must be activated to gain full activity; the protein structures are conserved through hundreds of millions of years of evolution; and some allosteric features arose with the early ancestor while others are more recent evolutionary events. The apoptotic caspases evolved from a common ancestor into two distinct subfamilies: monomers (initiator caspases) or dimers (effector caspases). Differences in activation mechanisms of the two subfamilies, and their oligomeric forms, play a central role in the regulation of apoptosis. Here, we examine changes in the folding landscape by characterizing human effector caspases and their common ancestor. The results show that the effector caspases unfold by a minimum three-state equilibrium model at pH 7.5, where the native dimer is in equilibrium with a partially folded monomeric (procaspase-7, common ancestor) or dimeric (procaspase-6) intermediate. In comparison, the unfolding pathway of procaspase-3 contains both oligomeric forms of the intermediate. Overall, the data show that the folding landscape was first established with the common ancestor and was then retained for >650 million years. Partially folded monomeric or dimeric intermediates in the ancestral ensemble provide mechanisms for evolutionary changes that affect stability of extant caspases. The conserved folding landscape allows for the fine-tuning of enzyme stability in a species-dependent manner while retaining the overall caspase-hemoglobinase fold.

scholarly journals Crosstalk of the Caspase Family and Mammalian Target of Rapamycin Signaling

2021 ◽  
Vol 22 (2) ◽  
pp. 817
Author(s):  
Junfang Yan ◽  
Yi Xie ◽  
Jing Si ◽  
Lu Gan ◽  
Hongyan Li ◽  
...  
Keyword(s):  
Cell Growth ◽  
Cell Survival ◽  
Cell Fate ◽  
Cellular Stress ◽  
Mammalian Target Of Rapamycin ◽  
Mtor Signaling ◽  
Target Of Rapamycin ◽  
Dependent Manner ◽  
Caspase Family ◽  
Mediate Cell

Cell can integrate the caspase family and mammalian target of rapamycin (mTOR) signaling in response to cellular stress triggered by environment. It is necessary here to elucidate the direct response and interaction mechanism between the two signaling pathways in regulating cell survival and determining cell fate under cellular stress. Members of the caspase family are crucial regulators of inflammation, endoplasmic reticulum stress response and apoptosis. mTOR signaling is known to mediate cell growth, nutrition and metabolism. For instance, over-nutrition can cause the hyperactivation of mTOR signaling, which is associated with diabetes. Nutrition deprivation can inhibit mTOR signaling via SH3 domain-binding protein 4. It is striking that Ras GTPase-activating protein 1 is found to mediate cell survival in a caspase-dependent manner against increasing cellular stress, which describes a new model of apoptosis. The components of mTOR signaling-raptor can be cleaved by caspases to control cell growth. In addition, mTOR is identified to coordinate the defense process of the immune system by suppressing the vitality of caspase-1 or regulating other interferon regulatory factors. The present review discusses the roles of the caspase family or mTOR pathway against cellular stress and generalizes their interplay mechanism in cell fate determination.

scholarly journals Decoding the temporal nature of brain GR activity in the NFκB signal transition leading to depressive-like behavior

2021 ◽  
Author(s):  
Young-Min Han ◽  
Min Sun Kim ◽  
Juyeong Jo ◽  
Daiha Shin ◽  
Seung-Hae Kwon ◽  
...  
Keyword(s):  
Inhibitory Action ◽  
Time Course ◽  
Molecular Mechanisms ◽  
Late Phase ◽  
Fine Tuning ◽  
Dependent Manner ◽  
Middle Phase ◽  
Temporal Shift

AbstractThe fine-tuning of neuroinflammation is crucial for brain homeostasis as well as its immune response. The transcription factor, nuclear factor-κ-B (NFκB) is a key inflammatory player that is antagonized via anti-inflammatory actions exerted by the glucocorticoid receptor (GR). However, technical limitations have restricted our understanding of how GR is involved in the dynamics of NFκB in vivo. In this study, we used an improved lentiviral-based reporter to elucidate the time course of NFκB and GR activities during behavioral changes from sickness to depression induced by a systemic lipopolysaccharide challenge. The trajectory of NFκB activity established a behavioral basis for the NFκB signal transition involved in three phases, sickness-early-phase, normal-middle-phase, and depressive-like-late-phase. The temporal shift in brain GR activity was differentially involved in the transition of NFκB signals during the normal and depressive-like phases. The middle-phase GR effectively inhibited NFκB in a glucocorticoid-dependent manner, but the late-phase GR had no inhibitory action. Furthermore, we revealed the cryptic role of basal GR activity in the early NFκB signal transition, as evidenced by the fact that blocking GR activity with RU486 led to early depressive-like episodes through the emergence of the brain NFκB activity. These results highlight the inhibitory action of GR on NFκB by the basal and activated hypothalamic-pituitary-adrenal (HPA)-axis during body-to-brain inflammatory spread, providing clues about molecular mechanisms underlying systemic inflammation caused by such as COVID-19 infection, leading to depression.

scholarly journals Regulation of Wnt Signaling by FOX Transcription Factors in Cancer

Cancers ◽  
2021 ◽  
Vol 13 (14) ◽  
pp. 3446
Author(s):  
Stefan Koch
Keyword(s):  
Transcription Factors ◽  
Wnt Signaling ◽  
Wnt Pathway ◽  
Treatment Options ◽  
Wnt Signaling Pathway ◽  
Tissue Homeostasis ◽  
Fine Tuning ◽  
Dependent Manner ◽  
Forkhead Box ◽  
Signaling Activity

Aberrant activation of the oncogenic Wnt signaling pathway is a hallmark of numerous types of cancer. However, in many cases, it is unclear how a chronically high Wnt signaling tone is maintained in the absence of activating pathway mutations. Forkhead box (FOX) family transcription factors are key regulators of embryonic development and tissue homeostasis, and there is mounting evidence that they act in part by fine-tuning the Wnt signaling output in a tissue-specific and context-dependent manner. Here, I review the diverse ways in which FOX transcription factors interact with the Wnt pathway, and how the ectopic reactivation of FOX proteins may affect Wnt signaling activity in various types of cancer. Many FOX transcription factors are partially functionally redundant and exhibit a highly restricted expression pattern, especially in adults. Thus, precision targeting of individual FOX proteins may lead to safe treatment options for Wnt-dependent cancers.

scholarly journals Comparing the folding landscapes of evolutionarily divergent procaspase-3

2022 ◽  
Author(s):  
Liqi Yao ◽  
Clay Clark
Keyword(s):  
Conformational Change ◽  
Common Ancestor ◽  
Folding Pathway ◽  
Free Energies ◽  
Folding Intermediates ◽  
Effector Caspases ◽  
The Common ◽  
Ph Dependent ◽  
Species Specific ◽  
Dimeric Intermediate

All caspases evolved from a common ancestor and subsequently developed into two general classes, inflammatory or apoptotic caspases. The caspase-hemoglobinase fold has been conserved throughout nearly one billion years of evolution and is utilized for both the monomeric and dimeric subfamilies of apoptotic caspases, called initiator and effector caspases, respectively. We compared the folding and assembly of procaspase-3b from zebrafish to that of human effector procaspases in order to examine the conservation of the folding landscape. Urea-induced equilibrium folding/unfolding of procaspase-3b showed a minimum three-state folding pathway, where the native dimer isomerizes to a partially folded dimeric intermediate, which then unfolds. A partially folded monomeric intermediate observed in the folding landscape of human procaspase-3 is not well-populated in zebrafish procaspase-3b. By comparing effector caspases from different species, we show that the effector procaspase dimer undergoes a pH-dependent conformational change, and that the conformational species in the folding landscape exhibit similar free energies. Together, the data show that the landscape for the caspase-hemoglobinase fold is conserved, yet it provides flexibility for species-specific stabilization or destabilization of folding intermediates resulting in changes in stability. The common pH-dependent conformational change in the native dimer, which yields an enzymatically inactive species, may provide an additional, albeit reversible, mechanism for controlling caspase activity in the cell.

scholarly journals An atomistic perspective on antibody-dependent cellular cytotoxicity quenching by core-fucosylation of IgG1 Fc N-glycans from enhanced sampling molecular dynamics

Glycobiology ◽  
2019 ◽  
Vol 30 (6) ◽  
pp. 407-414 ◽  
Author(s):  
Aoife Harbison ◽  
Elisa Fadda
Keyword(s):  
Molecular Dynamics ◽  
Binding Free Energy ◽  
Fine Tuning ◽  
Dependent Manner ◽  
Cellular Cytotoxicity ◽  
Antibody Dependent Cellular Cytotoxicity ◽  
Enhanced Sampling ◽  
Terminal Galactose ◽  
Autoimmune Conditions ◽  
Core Fucosylation

Abstract The immunoglobulin type G (IgG) Fc N-glycans are known to modulate the interaction with membrane-bound Fc γ receptors (FcγRs), fine-tuning the antibody’s effector function in a sequence-dependent manner. Particularly interesting in this respect are the roles of galactosylation, which levels are linked to autoimmune conditions and aging, of core fucosylation, which is known to reduce significantly the antibody-dependent cellular cytotoxicity (ADCC), and of sialylation, which also reduces antibody-dependent cellular cytotoxicity (ADCC) but only in the context of core-fucosylation. In this article, we provide an atomistic level perspective through enhanced sampling computer simulations, based on replica exchange molecular dynamics (REMD), to understand the molecular determinants linking the Fc N-glycans sequence to the observed IgG1 function. Our results indicate that the two symmetrically opposed N-glycans interact extensively through their core trimannose residues. At room temperature, the terminal galactose on the α (1–6) arm is restrained to the protein through a network of interactions that keep the arm outstretched; meanwhile, the α (1–3) arm extends toward the solvent where a terminal sialic acid remains fully accessible. We also find that the presence of core fucose interferes with the extended sialylated α (1–3) arm, altering its conformational propensity and as a consequence of steric hindrance, significantly enhancing the Fc dynamics. Furthermore, structural analysis shows that the core-fucose position within the Fc core obstructs the access of N162 glycosylated FcγRs very much like a “door-stop,” potentially decreasing the IgG/FcγR binding free energy. These results provide an atomistic level-of-detail framework for the design of high potency IgG1 Fc N-glycoforms.

scholarly journals IDH1 fine-tunes cap-dependent translation initiation

2019 ◽  
Vol 11 (10) ◽  
pp. 816-828 ◽  
Author(s):  
Lichao Liu ◽  
J Yuyang Lu ◽  
Fajin Li ◽  
Xudong Xing ◽  
Tong Li ◽  
...  
Keyword(s):  
Translation Initiation ◽  
Ribosomal Proteins ◽  
Rna Binding ◽  
Embryonic Stem ◽  
Mrna Translation ◽  
Fine Tuning ◽  
Start Codon ◽  
Metabolic Enzyme ◽  
Oxidative Decarboxylation ◽  
Dependent Manner

Abstract The metabolic enzyme isocitrate dehydrogenase 1 (IDH1) catalyzes the oxidative decarboxylation of isocitrate to α-ketoglutarate (α-KG). Its mutation often leads to aberrant gene expression in cancer. IDH1 was reported to bind thousands of RNA transcripts in a sequence-dependent manner; yet, the functional significance of this RNA-binding activity remains elusive. Here, we report that IDH1 promotes mRNA translation via direct associations with polysome mRNA and translation machinery. Comprehensive proteomic analysis in embryonic stem cells (ESCs) revealed striking enrichment of ribosomal proteins and translation regulators in IDH1-bound protein interactomes. We performed ribosomal profiling and analyzed mRNA transcripts that are associated with actively translating polysomes. Interestingly, knockout of IDH1 in ESCs led to significant downregulation of polysome-bound mRNA in IDH1 targets and subtle upregulation of ribosome densities at the start codon, indicating inefficient translation initiation upon loss of IDH1. Tethering IDH1 to a luciferase mRNA via the MS2-MBP system promotes luciferase translation, independently of the catalytic activity of IDH1. Intriguingly, IDH1 fails to enhance luciferase translation driven by an internal ribosome entry site. Together, these results reveal an unforeseen role of IDH1 in fine-tuning cap-dependent translation via the initiation step.

scholarly journals The Role of Autophagy in Pancreatic Cancer: From Bench to the Dark Bedside

Cells ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 1063 ◽  
Author(s):  
Kıvanç Görgülü ◽  
Kalliope N. Diakopoulos ◽  
Ezgi Kaya-Aksoy ◽  
Katrin J. Ciecielski ◽  
Jiaoyu Ai ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Fine Tuning ◽  
Cancer Tissue ◽  
Dependent Manner ◽  
Cancer Associated Fibroblasts ◽  
Preneoplastic Lesions ◽  
Pancreatic Cancer Tissue ◽  
Cancer Types ◽  
Initiation Stage

Pancreatic cancer is one of the deadliest cancer types urgently requiring effective therapeutic strategies. Autophagy occurs in several compartments of pancreatic cancer tissue including cancer cells, cancer associated fibroblasts, and immune cells where it can be subjected to a multitude of stimulatory and inhibitory signals fine-tuning its activity. Therefore, the effects of autophagy on pancreatic carcinogenesis and progression differ in a stage and context dependent manner. In the initiation stage autophagy hinders development of preneoplastic lesions; in the progression stage however, autophagy promotes tumor growth. This double-edged action of autophagy makes it a hard therapeutic target. Indeed, autophagy inhibitors have not yet shown survival improvements in clinical trials, indicating a need for better evaluation of existing results and smarter targeting techniques. Clearly, the role of autophagy in pancreatic cancer is complex and many aspects have to be considered when moving from the bench to the bedside.

scholarly journals tRNA-Derived Fragments Target the Ribosome and Function as Regulatory Non-Coding RNA inHaloferax volcanii

Archaea ◽  
2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Jennifer Gebetsberger ◽  
Marek Zywicki ◽  
Andrea Künzi ◽  
Norbert Polacek
Keyword(s):  
Gene Expression ◽  
Regulatory Networks ◽  
Ribosomal Subunit ◽  
Fine Tuning ◽  
Transferase Activity ◽  
Dependent Manner ◽  
Efficient Manner ◽  
Stress Dependent

Nonprotein coding RNA (ncRNA) molecules have been recognized recently as major contributors to regulatory networks in controlling gene expression in a highly efficient manner. These RNAs either originate from their individual transcription units or are processing products from longer precursor RNAs. For example, tRNA-derived fragments (tRFs) have been identified in all domains of life and represent a growing, yet functionally poorly understood, class of ncRNA candidates. Here we present evidence that tRFs from the halophilic archaeonHaloferax volcaniidirectly bind to ribosomes. In the presented genomic screen of the ribosome-associated RNome, a 26-residue-long fragment originating from the 5′ part of valine tRNA was by far the most abundant tRF. The Val-tRF is processed in a stress-dependent manner and was found to primarily target the small ribosomal subunitin vitroandin vivo. As a consequence of ribosome binding, Val-tRF reduces protein synthesis by interfering with peptidyl transferase activity. Therefore this tRF functions as ribosome-bound small ncRNA capable of regulating gene expression inH. volcaniiunder environmental stress conditions probably by fine tuning the rate of protein production.

scholarly journals Prediction and Characterization of RXLR Effectors in Pythium Species

2019 ◽  
Author(s):  
Gan Ai ◽  
Kun Yang ◽  
Yuee Tian ◽  
Wenwu Ye ◽  
Hai Zhu ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Plant Pathogens ◽  
Genome Rearrangement ◽  
Common Ancestor ◽  
De Novo ◽  
Protein Structures ◽  
Plant Diseases ◽  
Biocontrol Agents ◽  
Ecological Niches ◽  
Rxlr Effectors

AbstractBeing widely existed in oomycetes, the RXLR effector features conserved RXLR-dEER motifs in its N terminal. Every known Phytophthora or Hyaloperonospora pathogen harbors hundreds of RXLRs. In Pythium species, however, none of the RXLR effectors has been characterized yet. Here, we developed a stringent method for de novo identification of RXLRs and characterized 359 putative RXLR effectors from nine tested Pythium species. Phylogenetic analysis revealed a single superfamily formed by all oomycetous RXLRs, suggesting they descent from a common ancestor. RXLR effectors from Pythium and Phytophthora species exhibited similar sequence features, protein structures and genome locations. In particular, the mosquito biological agent P. guiyangense contains a significantly larger RXLR repertoire than the other eight Pythium species examined, which may result from gene duplication and genome rearrangement events as indicated by synteny analysis. Expression pattern analysis of RXLR-encoding genes in the plant pathogen P. ultimum detected transcripts from the vast majority of predicted RXLRs with some of them being induced at infection stages. One such RXLRs showed necrosis-inducing activity. Furthermore, all predicted RXLRs were cloned from two biocontrol agents P. oligandrum and P. periplocum. Three of them were found to encode effectors inducing defense response in Nicotiana benthamiana. Taken together, our findings represent the first complete synopsis of Pythium RXLR effectors, which provides critical clues on their evolutionary patterns as well as the mechanisms of their interactions with diverse hosts.Author summaryPathogens from the Pythium genus are widespread across multiple ecological niches. Most of them are soilborne plant pathogens whereas others cause infectious diseases in mammals. Some Pythium species can be used as biocontrol agents for plant diseases or mosquito management. Despite that phylogenetically close oomycete pathogens secrete RXLR effectors to enable infection, no RXLR protein was previously characterized in any Pythium species. Here we developed a stringent method to predict Pythium RXLR effectors and compared them with known RXLRs from other species. All oomycetous RXLRs form a huge superfamily, which indicates they may share a common ancestor. Our sequence analysis results suggest that the expansion of RXLR repertoire results from gene duplication and genome recombination events. We further demonstrated that most predicted Pythium RXLRs can be transcribed and some of them encode effectors exhibiting pathogenic or defense-inducing activities. This work expands our understanding of RXLR evolution in oomycetes in general, and provides novel insights into the molecular interactions between Pythium pathogens and their diverse hosts.

scholarly journals Loop size optimization: a new mechanism for protein stabilization

2016 ◽  
Author(s):  
Alessia Ruggiero ◽  
Nicole Balasco ◽  
Luciana Esposito ◽  
Luigi Vitagliano
Keyword(s):  
Secondary Structure ◽  
De Novo ◽  
Protein Structures ◽  
Protein Stabilization ◽  
Statistical Analyses ◽  
Fine Tuning ◽  
Marginal Stability ◽  
Loop Size ◽  
Thermophilic Organisms ◽  
The Impact

Motivation One of the fundamental issues in both chemistry and biology is the identification of the structural determinants that dictate protein folding and stability. The decoding of the folding code of protein structures would have a major impact on native structure prediction and on de novo design. This task is particularly difficult to achieve. Unlike synthetic polymers, protein structures combine complexity, fine-tuning and marginal stability. Despite these difficulties, in recent years major progresses have been made. A very recent breakthrough in the field is represented by the discovery of Baker and colleagues that the juxtaposition of basic secondary structure elements (α-helices and β-strands) follows well-defined rules ( Koga et al., 2012 ) . These investigations identified three fundamental rules for the preferences of βℓβ (strand-loop-strand), αℓβ (helix-loop-strand) and βℓα (strand-loop-helix) structural motifs. In particular, it was shown that the chirality of βℓβ and the orientation of βℓα/αℓβ strongly depend on the loop size. In this framework, we evaluated the impact of these rules on protein structures isolated from either (hyper)thermophilic or mesophilic organisms. We used the thioredoxin (Trx) system to experimentally validate the results emerged from the statistical analyses. Methods Statistical surveys Our statistical survey was based on the analyses of different structural databases made of proteins isolated from mesophilic or thermophilic organisms by assuming that the proteins of thermophilic species were on average more stable than those isolated from mesophilic ones. The adherence of these proteins to the rules identified by Baker and coworkers was evaluated. Experiments Wild-type E. coli Trx and a series of ad-hoc mutants were expressed and purified. The stability of these proteins was evaluated by CD spectroscopy. The structure of these variants was determined by X-ray crystallography. Results The statistical analyses indicate that in proteins isolated from thermophilic organisms better adhere to the Baker rules through the optimization of the size of the loop connecting secondary structure elements ( Balasco et al., 2013 ) . We then experimentally validated this mechanism using the thioredoxin isolated from E.coli (EcTrx), a widely characterized protein that has been used as a model in a large number of investigations ( Esposito et al., 2012 , Ruggiero et al., 2009 ) . Comparative analyses of loop sizes between EcTrx and Trx isolated from hyperthermophiles suggested that the size loop connecting helix 1 (α1) to strand 2 (β2) in EcTrx could be modified to better follow the rules. Chimeric variants were therefore prepared by replacing the loop of EcTrx with the corresponding ones present in the Trx isolated from Sulfolobus solfataricus and S. tokodaii. Abstract truncated at 3,000 characters - the full version is available in the pdf file

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